1
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Makwana R, Christ C, Marchi E, Harpell R, Lyon GJ. Longitudinal adaptive behavioral outcomes in Ogden syndrome by seizure status and therapeutic intervention. Am J Med Genet A 2024; 194:e63651. [PMID: 38747166 PMCID: PMC11315639 DOI: 10.1002/ajmg.a.63651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 04/16/2024] [Accepted: 04/27/2024] [Indexed: 05/28/2024]
Abstract
Ogden syndrome, also known as NAA10-related neurodevelopmental syndrome, is a rare genetic condition associated with pathogenic variants in the NAA10 N-terminal acetylation family of proteins. The condition was initially described in 2011 and is characterized by a range of neurologic symptoms, including intellectual disability and seizures, as well as developmental delays, psychiatric symptoms, congenital heart abnormalities, hypotonia, and others. Previously published articles have described the etiology and phenotype of Ogden syndrome, mostly with retrospective analyses; herein, we report prospective data concerning its progress over time. The current study involves a total of 58 distinct participants; of these, 43 caregivers were interviewed using the Vineland-3 and answered a survey regarding therapy and other questions, 10 of whom completed the Vineland-3 but did not answer the survey, and 5 participants who answered the survey but have not yet performed the Vineland-3 due to language constraints. The average age at the time of the most recent assessment was 12.4 years, with individuals ranging in age from 11 months to 40.2 years. Using Vineland-3 scores, we show decline in cognitive function over time in individuals with Ogden syndrome (n = 53). Sub-domain analysis found the decline to be present across all modalities. In addition, we describe the nature of seizures in this condition in greater detail, as well as investigate how already-available non-pharmaceutical therapies impact individuals with NAA10-related neurodevelopmental syndrome. Additional investigation between seizure and non-seizure groups showed no significant difference in adaptive behavior outcomes. A therapy investigation showed speech therapy to be the most commonly used therapy by individuals with NAA10-related neurodevelopmental syndrome, followed by occupational and physical therapy, with more severely affected individuals receiving more types of therapy than their less-severe counterparts. Early intervention analysis was only significantly effective for speech therapy, with analyses of all other therapies being non-significant. Our study portrays the decline in cognitive function over time of individuals within our cohort, independent of seizure status, and therapies being received, and highlights the urgent need for the development of effective treatments for Ogden syndrome.
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Affiliation(s)
- Rikhil Makwana
- Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York, United States of America
| | - Carolina Christ
- Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York, United States of America
| | - Elaine Marchi
- Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York, United States of America
| | - Randie Harpell
- Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York, United States of America
| | - Gholson J. Lyon
- Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York, United States of America
- George A. Jervis Clinic, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York, United States of America
- Biology PhD Program, The Graduate Center, The City University of New York, New York, United States of America
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2
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Woo H, Oh J, Cho YJ, Oh GT, Kim SY, Dan K, Han D, Lee JS, Kim T. N-terminal acetylation of Set1-COMPASS fine-tunes H3K4 methylation patterns. SCIENCE ADVANCES 2024; 10:eadl6280. [PMID: 38996018 PMCID: PMC11244526 DOI: 10.1126/sciadv.adl6280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 06/07/2024] [Indexed: 07/14/2024]
Abstract
H3K4 methylation by Set1-COMPASS (complex of proteins associated with Set1) is a conserved histone modification. Although it is critical for gene regulation, the posttranslational modifications of this complex that affect its function are largely unexplored. This study showed that N-terminal acetylation of Set1-COMPASS proteins by N-terminal acetyltransferases (NATs) can modulate H3K4 methylation patterns. Specifically, deleting NatA substantially decreased global H3K4me3 levels and caused the H3K4me2 peak in the 5' transcribed regions to shift to the promoters. NatA was required for N-terminal acetylation of three subunits of Set1-COMPASS: Shg1, Spp1, and Swd2. Moreover, deleting Shg1 or blocking its N-terminal acetylation via proline mutation of the target residue drastically reduced H3K4 methylation. Thus, NatA-mediated N-terminal acetylation of Shg1 shapes H3K4 methylation patterns. NatB also regulates H3K4 methylation, likely via N-terminal acetylation of the Set1-COMPASS protein Swd1. Thus, N-terminal acetylation of Set1-COMPASS proteins can directly fine-tune the functions of this complex, thereby substantially shaping H3K4 methylation patterns.
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Affiliation(s)
- Hyeonju Woo
- Department of Life Science and Multitasking Macrophage Research Center, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Junsoo Oh
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Yong-Joon Cho
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
- Multidimensional Genomics Research Center, Kangwon National University, Chuncheon, Republic of Korea
| | - Goo Taeg Oh
- Department of Life Science and Multitasking Macrophage Research Center, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Seon-Young Kim
- Korea Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Kisoon Dan
- Proteomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, Seoul 03082, Republic of Korea
| | - Dohyun Han
- Proteomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, Seoul 03082, Republic of Korea
- Department of Transdisciplinary Medicine, Seoul National University Hospital, Seoul 03082, Republic of Korea
- Department of Medicine, Seoul National University College of Medicine, Seoul 03082, Republic of Korea
| | - Jung-Shin Lee
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - TaeSoo Kim
- Department of Life Science and Multitasking Macrophage Research Center, Ewha Womans University, Seoul 03760, Republic of Korea
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Lyon GJ, Longo J, Garcia A, Inusa F, Marchi E, Shi D, Dörfel M, Arnesen T, Aldabe R, Lyons S, Nashat MA, Bolton D. Evaluating possible maternal effect lethality and genetic background effects in Naa10 knockout mice. PLoS One 2024; 19:e0301328. [PMID: 38713657 PMCID: PMC11075865 DOI: 10.1371/journal.pone.0301328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 03/14/2024] [Indexed: 05/09/2024] Open
Abstract
Amino-terminal (Nt-) acetylation (NTA) is a common protein modification, affecting approximately 80% of all human proteins. The human essential X-linked gene, NAA10, encodes for the enzyme NAA10, which is the catalytic subunit in the N-terminal acetyltransferase A (NatA) complex. There is extensive genetic variation in humans with missense, splice-site, and C-terminal frameshift variants in NAA10. In mice, Naa10 is not an essential gene, as there exists a paralogous gene, Naa12, that substantially rescues Naa10 knockout mice from embryonic lethality, whereas double knockouts (Naa10-/Y Naa12-/-) are embryonic lethal. However, the phenotypic variability in the mice is nonetheless quite extensive, including piebaldism, skeletal defects, small size, hydrocephaly, hydronephrosis, and neonatal lethality. Here we replicate these phenotypes with new genetic alleles in mice, but we demonstrate their modulation by genetic background and environmental effects. We cannot replicate a prior report of "maternal effect lethality" for heterozygous Naa10-/X female mice, but we do observe a small amount of embryonic lethality in the Naa10-/y male mice on the inbred genetic background in this different animal facility.
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Affiliation(s)
- Gholson J. Lyon
- Human Genetics Department, New York State Institute for Basic Research (IBR) in Developmental Disabilities, Staten Island, New York, United States of America
- Biology PhD Program, The Graduate Center, The City University of New York, New York, NY, United States of America
| | - Joseph Longo
- Human Genetics Department, New York State Institute for Basic Research (IBR) in Developmental Disabilities, Staten Island, New York, United States of America
| | - Andrew Garcia
- Human Genetics Department, New York State Institute for Basic Research (IBR) in Developmental Disabilities, Staten Island, New York, United States of America
- Biology PhD Program, The Graduate Center, The City University of New York, New York, NY, United States of America
| | - Fatima Inusa
- Human Genetics Department, New York State Institute for Basic Research (IBR) in Developmental Disabilities, Staten Island, New York, United States of America
| | - Elaine Marchi
- Human Genetics Department, New York State Institute for Basic Research (IBR) in Developmental Disabilities, Staten Island, New York, United States of America
| | - Daniel Shi
- Human Genetics Department, New York State Institute for Basic Research (IBR) in Developmental Disabilities, Staten Island, New York, United States of America
| | - Max Dörfel
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Woodbury, New York, United States of America
| | - Thomas Arnesen
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
- Department of Surgery, Haukeland University Hospital, Bergen, Norway
| | - Rafael Aldabe
- Division of Gene Therapy and Regulation of Gene Expression, CIMA, University of Navarra, Pamplona, Spain
| | - Scott Lyons
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Woodbury, New York, United States of America
| | - Melissa A. Nashat
- Human Genetics Department, New York State Institute for Basic Research (IBR) in Developmental Disabilities, Staten Island, New York, United States of America
| | - David Bolton
- Molecular Biology Department, New York State Institute for Basic Research (IBR) in Developmental Disabilities, Staten Island, New York, United States of America
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Venezian J, Bar-Yosef H, Ben-Arie Zilberman H, Cohen N, Kleifeld O, Fernandez-Recio J, Glaser F, Shiber A. Diverging co-translational protein complex assembly pathways are governed by interface energy distribution. Nat Commun 2024; 15:2638. [PMID: 38528060 DOI: 10.1038/s41467-024-46881-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 03/12/2024] [Indexed: 03/27/2024] Open
Abstract
Protein-protein interactions are at the heart of all cellular processes, with the ribosome emerging as a platform, orchestrating the nascent-chain interplay dynamics. Here, to study the characteristics governing co-translational protein folding and complex assembly, we combine selective ribosome profiling, imaging, and N-terminomics with all-atoms molecular dynamics. Focusing on conserved N-terminal acetyltransferases (NATs), we uncover diverging co-translational assembly pathways, where highly homologous subunits serve opposite functions. We find that only a few residues serve as "hotspots," initiating co-translational assembly interactions upon exposure at the ribosome exit tunnel. These hotspots are characterized by high binding energy, anchoring the entire interface assembly. Alpha-helices harboring hotspots are highly thermolabile, folding and unfolding during simulations, depending on their partner subunit to avoid misfolding. In vivo hotspot mutations disrupted co-translational complexation, leading to aggregation. Accordingly, conservation analysis reveals that missense NATs variants, causing neurodevelopmental and neurodegenerative diseases, disrupt putative hotspot clusters. Expanding our study to include phosphofructokinase, anthranilate synthase, and nucleoporin subcomplex, we employ AlphaFold-Multimer to model the complexes' complete structures. Computing MD-derived interface energy profiles, we find similar trends. Here, we propose a model based on the distribution of interface energy as a strong predictor of co-translational assembly.
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Affiliation(s)
- Johannes Venezian
- Faculty of Biology, Technion Israel institute of Technology, Haifa, Israel
| | - Hagit Bar-Yosef
- Faculty of Biology, Technion Israel institute of Technology, Haifa, Israel
| | | | - Noam Cohen
- Faculty of Biology, Technion Israel institute of Technology, Haifa, Israel
| | - Oded Kleifeld
- Faculty of Biology, Technion Israel institute of Technology, Haifa, Israel
| | - Juan Fernandez-Recio
- Instituto de Ciencias de la Vid y del Vino (ICVV), CSIC-Universidad de La Rioja-Gobierno de La Rioja, Logroño, Spain
| | - Fabian Glaser
- Lorry I. Lokey Interdisciplinary Center for Life Sciences & Engineering, Haifa, Israel
| | - Ayala Shiber
- Faculty of Biology, Technion Israel institute of Technology, Haifa, Israel.
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Makwana R, Christ C, Marchi E, Harpell R, Lyon GJ. Longitudinal Adaptive Behavioral Outcomes in Ogden Syndrome by Seizure Status and Therapeutic Intervention. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.02.23.24303144. [PMID: 38585745 PMCID: PMC10996826 DOI: 10.1101/2024.02.23.24303144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Ogden syndrome, also known as NAA10-related neurodevelopmental syndrome, is a rare genetic condition associated with pathogenic variants in the NAA10 N-terminal acetylation family of proteins. The condition was initially described in 2011, and is characterized by a range of neurologic symptoms, including intellectual disability and seizures, as well as developmental delays, psychiatric symptoms, congenital heart abnormalities, hypotonia and others. Previously published articles have described the etiology and phenotype of Ogden syndrome, mostly with retrospective analyses; herein, we report prospective data concerning its progress over time. Additionally, we describe the nature of seizures in this condition in greater detail, as well as investigate how already-available non-pharmaceutical therapies impact individuals with NAA10-related neurodevelopmental syndrome. Using Vineland-3 scores, we show decline in cognitive function over time in individuals with Ogden syndrome. Sub-domain analysis found the decline to be present across all modalities. Additional investigation between seizure and non-seizure groups showed no significant difference in adaptive behavior outcomes. Therapy investigation showed speech therapy to be the most commonly used therapy by individuals with NAA10-related neurodevelopmental syndrome, followed by occupational and physical therapy. with more severely affected individuals receiving more types of therapy than their less-severe counterparts. Early intervention analysis was only significantly effective for speech therapy, with analyses of all other therapies being non-significant. Our study portrays the decline in cognitive function over time of individuals within our cohort, independent of seizure status and therapies being received, and highlights the urgent need for the development of effective treatments for Ogden syndrome.
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Affiliation(s)
- Rikhil Makwana
- Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York, United States of America
| | - Carolina Christ
- Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York, United States of America
| | - Elaine Marchi
- Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York, United States of America
| | - Randie Harpell
- Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York, United States of America
| | - Gholson J. Lyon
- Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York, United States of America
- George A. Jervis Clinic, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York, United States of America
- Biology PhD Program, The Graduate Center, The City University of New York, New York, United States of America
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Li F, Wang W, Li Y, Liu X, Zhu Z, Tang J, Hu Y. NAA10 gene related Ogden syndrome with obstructive hypertrophic cardiomyopathy: A rare case report. Medicine (Baltimore) 2024; 103:e36034. [PMID: 38335407 PMCID: PMC10860986 DOI: 10.1097/md.0000000000036034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 10/19/2023] [Indexed: 02/12/2024] Open
Abstract
RATIONALE Ogden syndrome is an exceptionally rare X-linked disease caused by mutations in the NAA10 gene. Reported cases of this syndrome are approximately 20 children and are associated with facial dysmorphism, growth delay, developmental disorders, congenital heart disease, and arrhythmia. PATIENT CONCERNS We present the clinical profile of a 3-year-old girl with Ogden syndrome carrying a de novo NAA10 variant [NM_003491:c.247C>T, p.(Arg83Cys)]. During infancy, she exhibited features such as left ventricular hypertrophy, protruding eyeballs, and facial deformities. DIAGNOSIS Clinical diagnosis included Ogden syndrome, congenital heart disease (obstructive hypertrophic cardiomyopathy, left ventricular outflow tract obstruction, mitral valve disease, tricuspid valve regurgitation), tonsillar and adenoidal hypertrophy, and speech and language delay. INTERVENTIONS The girl was considered to have hypertrophic cardiomyopathy (HCM) and received oral metoprolol as a treatment for HCM at our hospital. The drug treatment effect was not ideal, and her hypertrophy myocardial symptoms were aggravated and she had to be hospitalized for surgery. OUTCOMES The girl underwent a modified Morrow procedure under cardiopulmonary bypass and experienced a favorable postoperative recovery. No pulmonary infections or significant complications were observed during this period. The patient's family expressed satisfaction with the treatment process. LESSONS The case emphasizes the HCM of Odgen syndrome, and early surgery should be performed if drug treatment is ineffective.
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Affiliation(s)
- Feihong Li
- Department of Anesthesiology, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Wenyang Wang
- Department of Anesthesiology, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yazhou Li
- Department of Clinical Laboratory, Huadong Hospital, Fudan University, Shanghai, China
| | - Xiwang Liu
- Department of Cardiac Surgery, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhirui Zhu
- Department of Anesthesiology, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jian Tang
- Department of Anesthesiology, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yaoqin Hu
- Department of Anesthesiology, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Lyon GJ, Longo J, Garcia A, Inusa F, Marchi E, Shi D, Dörfel M, Arnesen T, Aldabe R, Lyons S, Nashat MA, Bolton D. Evaluating possible maternal effect lethality and genetic background effects in Naa10 knockout mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.27.538618. [PMID: 37163119 PMCID: PMC10168333 DOI: 10.1101/2023.04.27.538618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Amino-terminal (Nt-) acetylation (NTA) is a common protein modification, affecting approximately 80% of all human proteins. The human essential X-linked gene, NAA10, encodes for the enzyme NAA10, which is the catalytic subunit in the N-terminal acetyltransferase A (NatA) complex. There is extensive genetic variation in humans with missense, splice-site, and C-terminal frameshift variants in NAA10. In mice, Naa10 is not an essential gene, as there exists a paralogous gene, Naa12, that substantially rescues Naa10 knockout mice from embryonic lethality, whereas double knockouts (Naa10-/Y Naa12-/-) are embryonic lethal. However, the phenotypic variability in the mice is nonetheless quite extensive, including piebaldism, skeletal defects, small size, hydrocephaly, hydronephrosis, and neonatal lethality. Here we replicate these phenotypes with new genetic alleles in mice, but we demonstrate their modulation by genetic background and environmental effects. We cannot replicate a prior report of "maternal effect lethality" for heterozygous Naa10-/X female mice, but we do observe a small amount of embryonic lethality in the Naa10-/Y male mice on the inbred genetic background in this different animal facility.
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Affiliation(s)
- Gholson J. Lyon
- Human Genetics Department, New York State Institute for Basic Research (IBR) in Developmental Disabilities, Staten Island, New York, USA
- Biology PhD Program, The Graduate Center, The City University of New York, New York, USA
| | - Joseph Longo
- Human Genetics Department, New York State Institute for Basic Research (IBR) in Developmental Disabilities, Staten Island, New York, USA
| | - Andrew Garcia
- Human Genetics Department, New York State Institute for Basic Research (IBR) in Developmental Disabilities, Staten Island, New York, USA
- Biology PhD Program, The Graduate Center, The City University of New York, New York, USA
| | - Fatima Inusa
- Human Genetics Department, New York State Institute for Basic Research (IBR) in Developmental Disabilities, Staten Island, New York, USA
| | - Elaine Marchi
- Human Genetics Department, New York State Institute for Basic Research (IBR) in Developmental Disabilities, Staten Island, New York, USA
| | - Daniel Shi
- Human Genetics Department, New York State Institute for Basic Research (IBR) in Developmental Disabilities, Staten Island, New York, USA
| | - Max Dörfel
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Woodbury, New York, USA
| | - Thomas Arnesen
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
- Department of Surgery, Haukeland University Hospital, Bergen, Norway
| | - Rafael Aldabe
- Division of Gene Therapy and Regulation of Gene Expression, CIMA, University of Navarra, Pamplona, Spain
| | - Scott Lyons
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Woodbury, New York, USA
| | - Melissa A. Nashat
- Human Genetics Department, New York State Institute for Basic Research (IBR) in Developmental Disabilities, Staten Island, New York, USA
| | - David Bolton
- Molecular Biology Department, New York State Institute for Basic Research (IBR) in Developmental Disabilities, Staten Island, New York, USA
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Nashed S, El Barbry H, Benchouaia M, Dijoux-Maréchal A, Delaveau T, Ruiz-Gutierrez N, Gaulier L, Tribouillard-Tanvier D, Chevreux G, Le Crom S, Palancade B, Devaux F, Laine E, Garcia M. Functional mapping of N-terminal residues in the yeast proteome uncovers novel determinants for mitochondrial protein import. PLoS Genet 2023; 19:e1010848. [PMID: 37585488 PMCID: PMC10482271 DOI: 10.1371/journal.pgen.1010848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 09/06/2023] [Accepted: 06/29/2023] [Indexed: 08/18/2023] Open
Abstract
N-terminal ends of polypeptides are critical for the selective co-translational recruitment of N-terminal modification enzymes. However, it is unknown whether specific N-terminal signatures differentially regulate protein fate according to their cellular functions. In this work, we developed an in-silico approach to detect functional preferences in cellular N-terminomes, and identified in S. cerevisiae more than 200 Gene Ontology terms with specific N-terminal signatures. In particular, we discovered that Mitochondrial Targeting Sequences (MTS) show a strong and specific over-representation at position 2 of hydrophobic residues known to define potential substrates of the N-terminal acetyltransferase NatC. We validated mitochondrial precursors as co-translational targets of NatC by selective purification of translating ribosomes, and found that their N-terminal signature is conserved in Saccharomycotina yeasts. Finally, systematic mutagenesis of the position 2 in a prototypal yeast mitochondrial protein confirmed its critical role in mitochondrial protein import. Our work highlights the hydrophobicity of MTS N-terminal residues and their targeting by NatC as important features for the definition of the mitochondrial proteome, providing a molecular explanation for mitochondrial defects observed in yeast or human NatC-depleted cells. Functional mapping of N-terminal residues thus has the potential to support the discovery of novel mechanisms of protein regulation or targeting.
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Affiliation(s)
- Salomé Nashed
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
| | - Houssam El Barbry
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
| | - Médine Benchouaia
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
| | - Angélie Dijoux-Maréchal
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
| | - Thierry Delaveau
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
| | - Nadia Ruiz-Gutierrez
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
| | - Lucie Gaulier
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
| | | | | | - Stéphane Le Crom
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
| | | | - Frédéric Devaux
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
| | - Elodie Laine
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
| | - Mathilde Garcia
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
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Lyon GJ, Vedaie M, Beisheim T, Park A, Marchi E, Gottlieb L, Hsieh TC, Klinkhammer H, Sandomirsky K, Cheng H, Starr LJ, Preddy I, Tseng M, Li Q, Hu Y, Wang K, Carvalho A, Martinez F, Caro-Llopis A, Gavin M, Amble K, Krawitz P, Marmorstein R, Herr-Israel E. Expanding the phenotypic spectrum of NAA10-related neurodevelopmental syndrome and NAA15-related neurodevelopmental syndrome. Eur J Hum Genet 2023; 31:824-833. [PMID: 37130971 PMCID: PMC10325952 DOI: 10.1038/s41431-023-01368-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 02/11/2023] [Accepted: 04/17/2023] [Indexed: 05/04/2023] Open
Abstract
Amino-terminal (Nt-) acetylation (NTA) is a common protein modification, affecting 80% of cytosolic proteins in humans. The human essential gene, NAA10, encodes for the enzyme NAA10, which is the catalytic subunit in the N-terminal acetyltransferase A (NatA) complex, also including the accessory protein, NAA15. The full spectrum of human genetic variation in this pathway is currently unknown. Here we reveal the genetic landscape of variation in NAA10 and NAA15 in humans. Through a genotype-first approach, one clinician interviewed the parents of 56 individuals with NAA10 variants and 19 individuals with NAA15 variants, which were added to all known cases (N = 106 for NAA10 and N = 66 for NAA15). Although there is clinical overlap between the two syndromes, functional assessment demonstrates that the overall level of functioning for the probands with NAA10 variants is significantly lower than the probands with NAA15 variants. The phenotypic spectrum includes variable levels of intellectual disability, delayed milestones, autism spectrum disorder, craniofacial dysmorphology, cardiac anomalies, seizures, and visual abnormalities (including cortical visual impairment and microphthalmia). One female with the p.Arg83Cys variant and one female with an NAA15 frameshift variant both have microphthalmia. The frameshift variants located toward the C-terminal end of NAA10 have much less impact on overall functioning, whereas the females with the p.Arg83Cys missense in NAA10 have substantial impairment. The overall data are consistent with a phenotypic spectrum for these alleles, involving multiple organ systems, thus revealing the widespread effect of alterations of the NTA pathway in humans.
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Affiliation(s)
- Gholson J Lyon
- Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USA.
- George A. Jervis Clinic, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USA.
- Biology PhD Program, The Graduate Center, The City University of New York, New York, NY, USA.
| | - Marall Vedaie
- Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USA
| | - Travis Beisheim
- Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USA
| | - Agnes Park
- Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USA
| | - Elaine Marchi
- Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USA
| | - Leah Gottlieb
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Tzung-Chien Hsieh
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Hannah Klinkhammer
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
- Institute for Medical Biometry, Informatics and Epidemiology, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Katherine Sandomirsky
- Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USA
| | | | - Lois J Starr
- Department of Pediatrics, University of Nebraska Medical Center, Omaha, NE, USA
| | - Isabelle Preddy
- Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USA
| | - Marcellus Tseng
- Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USA
| | - Quan Li
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, M5G2C1, Canada
| | - Yu Hu
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Ana Carvalho
- Department of Medical Genetics, Pediatric Hospital, Coimbra Hospital and University Centre, Coimbra, Portugal
| | - Francisco Martinez
- Unidad de Genetica, Hospital Universitario y Politecnico La Fe, 46026, Valencia, Spain
| | - Alfonso Caro-Llopis
- Grupo de Investigacion Traslacional en Genetica, Instituto de Investigacion Sanitaria La Fe, 46026, Valencia, Spain
| | - Maureen Gavin
- George A. Jervis Clinic, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USA
| | - Karen Amble
- George A. Jervis Clinic, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USA
| | - Peter Krawitz
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Ronen Marmorstein
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ellen Herr-Israel
- George A. Jervis Clinic, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USA
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10
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Fernández E, Bogaert A, Timmerman E, Staes A, Impens F, Gevaert K. A Strong Cation Exchange Chromatography Protocol for Examining N-Terminal Proteoforms. Methods Mol Biol 2022; 2477:293-309. [PMID: 35524124 DOI: 10.1007/978-1-0716-2257-5_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Especially in eukaryotes, the N-terminal acetylation status of a protein reveals translation initiation sites and substrate specificities and activities of N-terminal acetyltransferases (NATs). Here, we discuss a bottom-up proteomics protocol for the enrichment of N-terminal peptides via strong cation exchange chromatography. This protocol is based on depleting internal tryptic peptides from proteome digests through their retention on strong cation exchangers, leaving N-terminally acetylated/blocked peptides enriched among the nonretained peptides. As such, one can identify novel N-terminal proteoforms and quantify the degree of N-terminal protein acetylation.
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Affiliation(s)
- Esperanza Fernández
- VIB Center for Medical Biotechnology, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Annelies Bogaert
- VIB Center for Medical Biotechnology, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Evy Timmerman
- VIB Center for Medical Biotechnology, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- VIB Proteomics Core, Ghent, Belgium
| | - An Staes
- VIB Center for Medical Biotechnology, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- VIB Proteomics Core, Ghent, Belgium
| | - Francis Impens
- VIB Center for Medical Biotechnology, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- VIB Proteomics Core, Ghent, Belgium
| | - Kris Gevaert
- VIB Center for Medical Biotechnology, Ghent, Belgium.
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
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11
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Van Damme P. Charting the N-Terminal Acetylome: A Comprehensive Map of Human NatA Substrates. Int J Mol Sci 2021; 22:ijms221910692. [PMID: 34639033 PMCID: PMC8509067 DOI: 10.3390/ijms221910692] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/10/2021] [Accepted: 09/29/2021] [Indexed: 11/29/2022] Open
Abstract
N-terminal acetylation (Nt-acetylation) catalyzed by conserved N-terminal acetyltransferases or NATs embodies a modification with one of the highest stoichiometries reported for eukaryotic protein modifications to date. Comprising the catalytic N-alpha acetyltransferase (NAA) subunit NAA10 plus the ribosome anchoring regulatory subunit NAA15, NatA represents the major acetyltransferase complex with up to 50% of all mammalian proteins representing potential substrates. Largely in consequence of the essential nature of NatA and its high enzymatic activity, its experimentally confirmed mammalian substrate repertoire remained poorly charted. In this study, human NatA knockdown conditions achieving near complete depletion of NAA10 and NAA15 expression resulted in lowered Nt-acetylation of over 25% out of all putative NatA targets identified, representing an up to 10-fold increase in the reported number of substrate N-termini affected upon human NatA perturbation. Besides pointing to less efficient NatA substrates being prime targets, several putative NatE substrates were shown to be affected upon human NatA knockdown. Intriguingly, next to a lowered expression of ribosomal proteins and proteins constituting the eukaryotic 48S preinitiation complex, steady-state levels of protein N-termini additionally point to NatA Nt-acetylation deficiency directly impacting protein stability of knockdown affected targets.
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Affiliation(s)
- Petra Van Damme
- iRIP Unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
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12
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Kweon HY, Lee MN, Dorfel M, Seo S, Gottlieb L, PaPazyan T, McTiernan N, Ree R, Bolton D, Garcia A, Flory M, Crain J, Sebold A, Lyons S, Ismail A, Marchi E, Sonn SK, Jeong SJ, Jeon S, Ju S, Conway SJ, Kim T, Kim HS, Lee C, Roh TY, Arnesen T, Marmorstein R, Oh GT, Lyon GJ. Naa12 compensates for Naa10 in mice in the amino-terminal acetylation pathway. eLife 2021; 10:e65952. [PMID: 34355692 PMCID: PMC8376253 DOI: 10.7554/elife.65952] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 08/05/2021] [Indexed: 01/17/2023] Open
Abstract
Amino-terminal acetylation is catalyzed by a set of N-terminal acetyltransferases (NATs). The NatA complex (including X-linked Naa10 and Naa15) is the major acetyltransferase, with 40-50% of all mammalian proteins being potential substrates. However, the overall role of amino-terminal acetylation on a whole-organism level is poorly understood, particularly in mammals. Male mice lacking Naa10 show no globally apparent in vivo amino-terminal acetylation impairment and do not exhibit complete embryonic lethality. Rather Naa10 nulls display increased neonatal lethality, and the majority of surviving undersized mutants exhibit a combination of hydrocephaly, cardiac defects, homeotic anterior transformation, piebaldism, and urogenital anomalies. Naa12 is a previously unannotated Naa10-like paralog with NAT activity that genetically compensates for Naa10. Mice deficient for Naa12 have no apparent phenotype, whereas mice deficient for Naa10 and Naa12 display embryonic lethality. The discovery of Naa12 adds to the currently known machinery involved in amino-terminal acetylation in mice.
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Affiliation(s)
- Hyae Yon Kweon
- Department of Life Science and College of Natural Sciences, Ewha Womans UniversitySeoulRepublic of Korea
| | - Mi-Ni Lee
- Department of Life Science and College of Natural Sciences, Ewha Womans UniversitySeoulRepublic of Korea
- Laboratory Animal Resource Center Korea ResearchInstitute of Bioscience and BiotechnologyChungbukRepublic of Korea
| | - Max Dorfel
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor LaboratoryWoodburyUnited States
| | - Seungwoon Seo
- Department of Life Science and College of Natural Sciences, Ewha Womans UniversitySeoulRepublic of Korea
| | - Leah Gottlieb
- Department of Chemistry, University of PennsylvaniaPhiladelphiaUnited States
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Thomas PaPazyan
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor LaboratoryWoodburyUnited States
| | - Nina McTiernan
- Department of Biomedicine, University of BergenBergenNorway
| | - Rasmus Ree
- Department of Biomedicine, University of BergenBergenNorway
| | - David Bolton
- Department of Molecular Biology, New York State Institute for Basic Research in Developmental DisabilitiesStaten IslandUnited States
| | - Andrew Garcia
- Department of Human Genetics, New York State Institute for Basic Research in Developmental DisabilitiesStaten IslandUnited States
| | - Michael Flory
- Research Design and Analysis Service, New York State Institute for Basic Research in Developmental DisabilitiesStaten IslandUnited States
| | - Jonathan Crain
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor LaboratoryWoodburyUnited States
| | - Alison Sebold
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor LaboratoryWoodburyUnited States
| | - Scott Lyons
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor LaboratoryWoodburyUnited States
| | - Ahmed Ismail
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor LaboratoryWoodburyUnited States
| | - Elaine Marchi
- Department of Human Genetics, New York State Institute for Basic Research in Developmental DisabilitiesStaten IslandUnited States
| | - Seong-keun Sonn
- Department of Life Science and College of Natural Sciences, Ewha Womans UniversitySeoulRepublic of Korea
| | - Se-Jin Jeong
- Center for Cardiovascular Research, Washington University School of MedicineSaint LouisUnited States
| | - Sejin Jeon
- Department of Life Science and College of Natural Sciences, Ewha Womans UniversitySeoulRepublic of Korea
| | - Shinyeong Ju
- Center for Theragnosis, Korea Institute of Science and TechnologySeoulRepublic of Korea
| | - Simon J Conway
- Herman B. Wells Center for Pediatric Research, Indiana University School of MedicineIndianapolisUnited States
| | - Taesoo Kim
- Department of Life Science and College of Natural Sciences, Ewha Womans UniversitySeoulRepublic of Korea
| | - Hyun-Seok Kim
- Department of Life Science and College of Natural Sciences, Ewha Womans UniversitySeoulRepublic of Korea
| | - Cheolju Lee
- Center for Theragnosis, Korea Institute of Science and TechnologySeoulRepublic of Korea
- Department of Converging Science and Technology, KHU-KIST, Kyung Hee UniversitySeoulRepublic of Korea
| | - Tae-Young Roh
- Department of Life Sciences, Pohang University of Science and TechnologyPohangRepublic of Korea
| | - Thomas Arnesen
- Department of Biomedicine, University of BergenBergenNorway
- Department of Biological Sciences, University of BergenBergenNorway
- Department of Surgery, Haukeland University HospitalBergenNorway
| | - Ronen Marmorstein
- Department of Chemistry, University of PennsylvaniaPhiladelphiaUnited States
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Goo Taeg Oh
- Department of Life Science and College of Natural Sciences, Ewha Womans UniversitySeoulRepublic of Korea
| | - Gholson J Lyon
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor LaboratoryWoodburyUnited States
- Department of Human Genetics, New York State Institute for Basic Research in Developmental DisabilitiesStaten IslandUnited States
- Biology PhD Program, The Graduate Center, The City University of New YorkNew YorkUnited States
- George A. Jervis Clinic, New York State Institute for Basic Research in Developmental DisabilitiesStaten IslandUnited States
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13
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Morrison J, Altuwaijri NK, Brønstad K, Aksnes H, Alsaif HS, Evans A, Hashem M, Wheeler PG, Webb BD, Alkuraya FS, Arnesen T. Missense NAA20 variants impairing the NatB protein N-terminal acetyltransferase cause autosomal recessive developmental delay, intellectual disability, and microcephaly. Genet Med 2021; 23:2213-2218. [PMID: 34230638 PMCID: PMC8553619 DOI: 10.1038/s41436-021-01264-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 11/26/2022] Open
Abstract
Purpose N-terminal acetyltransferases modify proteins by adding an acetyl
moiety to the first amino acid and are vital for protein and cell function. The
NatB complex acetylates 20% of the human proteome and is composed of the
catalytic subunit NAA20 and the auxiliary subunit NAA25. In five individuals
with overlapping phenotypes, we identified recessive homozygous missense
variants in NAA20. Methods Two different NAA20 variants were
identified in affected individuals in two consanguineous families by exome and
genome sequencing. Biochemical studies were employed to assess the impact of the
NAA20 variants on NatB complex formation
and catalytic activity. Results Two homozygous variants, NAA20
p.Met54Val and p.Ala80Val (GenBank: NM_016100.4, c.160A>G and
c.239C>T), segregated with affected individuals in two unrelated
families presenting with developmental delay, intellectual disability, and
microcephaly. Both NAA20-M54V and NAA20-A80V were impaired in their capacity to
form a NatB complex with NAA25, and in vitro acetylation assays revealed reduced
catalytic activities toward different NatB substrates. Thus, both NAA20 variants
are impaired in their ability to perform cellular NatB-mediated N-terminal
acetylation. Conclusion We present here a report of pathogenic NAA20 variants causing human disease and data supporting an
essential role for NatB-mediated N-terminal acetylation in human development and
physiology. Graphical Abstract ![]()
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Affiliation(s)
| | - Norah K Altuwaijri
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | | | | | - Hessa S Alsaif
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Anthony Evans
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mais Hashem
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | | | - Bryn D Webb
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Thomas Arnesen
- Department of Biomedicine, University of Bergen, Bergen, Norway. .,Department of Biological Sciences, University of Bergen, Bergen, Norway. .,Department of Surgery, Haukeland University Hospital, Bergen, Norway.
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14
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Jonckheere V, Van Damme P. N-Terminal Acetyltransferase Naa40p Whereabouts Put into N-Terminal Proteoform Perspective. Int J Mol Sci 2021; 22:ijms22073690. [PMID: 33916271 PMCID: PMC8037211 DOI: 10.3390/ijms22073690] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/28/2021] [Accepted: 03/28/2021] [Indexed: 11/21/2022] Open
Abstract
The evolutionary conserved N-alpha acetyltransferase Naa40p is among the most selective N-terminal acetyltransferases (NATs) identified to date. Here we identified a conserved N-terminally truncated Naa40p proteoform named Naa40p25 or short Naa40p (Naa40S). Intriguingly, although upon ectopic expression in yeast, both Naa40p proteoforms were capable of restoring N-terminal acetylation of the characterized yeast histone H2A Naa40p substrate, the Naa40p histone H4 substrate remained N-terminally free in human haploid cells specifically deleted for canonical Naa40p27 or 237 amino acid long Naa40p (Naa40L), but expressing Naa40S. Interestingly, human Naa40L and Naa40S displayed differential expression and subcellular localization patterns by exhibiting a principal nuclear and cytoplasmic localization, respectively. Furthermore, Naa40L was shown to be N-terminally myristoylated and to interact with N-myristoyltransferase 1 (NMT1), implicating NMT1 in steering Naa40L nuclear import. Differential interactomics data obtained by biotin-dependent proximity labeling (BioID) further hints to context-dependent roles of Naa40p proteoforms. More specifically, with Naa40S representing the main co-translationally acting actor, the interactome of Naa40L was enriched for nucleolar proteins implicated in ribosome biogenesis and the assembly of ribonucleoprotein particles, overall indicating a proteoform-specific segregation of previously reported Naa40p activities. Finally, the yeast histone variant H2A.Z and the transcriptionally regulatory protein Lge1 were identified as novel Naa40p substrates, expanding the restricted substrate repertoire of Naa40p with two additional members and further confirming Lge1 as being the first redundant yNatA and yNatD substrate identified to date.
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15
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McTiernan N, Gill H, Prada CE, Pachajoa H, Lores J, Arnesen T. NAA10 p.(N101K) disrupts N-terminal acetyltransferase complex NatA and is associated with developmental delay and hemihypertrophy. Eur J Hum Genet 2021; 29:280-288. [PMID: 32973342 PMCID: PMC7868364 DOI: 10.1038/s41431-020-00728-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 07/31/2020] [Accepted: 09/08/2020] [Indexed: 01/23/2023] Open
Abstract
Nearly half of all human proteins are acetylated at their N-termini by the NatA N-terminal acetyltransferase complex. NAA10 is evolutionarily conserved as the catalytic subunit of NatA in complex with NAA15, but may also have NatA-independent functions. Several NAA10 variants are associated with genetic disorders. The phenotypic spectrum includes developmental delay, intellectual disability, and cardiac abnormalities. Here, we have identified the previously undescribed NAA10 c.303C>A and c.303C>G p.(N101K) variants in two unrelated girls. These girls have developmental delay, but they both also display hemihypertrophy a feature normally not observed or registered among these cases. Functional studies revealed that NAA10 p.(N101K) is completely impaired in its ability to bind NAA15 and to form an enzymatically active NatA complex. In contrast, the integrity of NAA10 p.(N101K) as a monomeric acetyltransferase is intact. Thus, this NAA10 variant may represent the best example of the impact of NatA mediated N-terminal acetylation, isolated from other potential NAA10-mediated cellular functions and may provide important insights into the phenotypes observed in individuals expressing pathogenic NAA10 variants.
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Affiliation(s)
- Nina McTiernan
- Department of Biomedicine, University of Bergen, N-5020, Bergen, Norway
| | - Harinder Gill
- Department of Medical Genetics, Children's and Women's Health Centre of British Columbia, Vancouver, BC, V6H 3N1, Canada
| | - Carlos E Prada
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, 45229, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, 45229, Cincinnati, OH, USA
- Centro de Medicina Genomica y Metabolismo, Fundacion Cardiovascular de Colombia, Floridablanca, Colombia
| | - Harry Pachajoa
- Centro de Investigaciones en Anomalías Congénitas y Enfermedades Raras Universidad Icesi, Cali, Colombia
- Fundación Clínica Valle del Lili, Cali, Colombia
| | - Juliana Lores
- Centro de Investigaciones en Anomalías Congénitas y Enfermedades Raras Universidad Icesi, Cali, Colombia
- Fundación Clínica Valle del Lili, Cali, Colombia
| | - Thomas Arnesen
- Department of Biomedicine, University of Bergen, N-5020, Bergen, Norway.
- Department of Biological Sciences, University of Bergen, N-5020, Bergen, Norway.
- Department of Surgery, Haukeland University Hospital, N-5021, Bergen, Norway.
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16
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N α-terminal acetylation of proteins by NatA and NatB serves distinct physiological roles in Saccharomyces cerevisiae. Cell Rep 2021; 34:108711. [PMID: 33535049 DOI: 10.1016/j.celrep.2021.108711] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 10/10/2020] [Accepted: 01/09/2021] [Indexed: 11/22/2022] Open
Abstract
N-terminal (Nt) acetylation is a highly prevalent co-translational protein modification in eukaryotes, catalyzed by at least five Nt acetyltransferases (Nats) with differing specificities. Nt acetylation has been implicated in protein quality control, but its broad biological significance remains elusive. We investigate the roles of the two major Nats of S. cerevisiae, NatA and NatB, by performing transcriptome, translatome, and proteome profiling of natAΔ and natBΔ mutants. Our results reveal a range of NatA- and NatB-specific phenotypes. NatA is implicated in systemic adaptation control, because natAΔ mutants display altered expression of transposons, sub-telomeric genes, pheromone response genes, and nuclear genes encoding mitochondrial ribosomal proteins. NatB predominantly affects protein folding, because natBΔ mutants, to a greater extent than natA mutants, accumulate protein aggregates, induce stress responses, and display reduced fitness in the absence of the ribosome-associated chaperone Ssb. These phenotypic differences indicate that controlling Nat activities may serve to elicit distinct cellular responses.
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17
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Weidenhausen J, Kopp J, Armbruster L, Wirtz M, Lapouge K, Sinning I. Structural and functional characterization of the N-terminal acetyltransferase Naa50. Structure 2021; 29:413-425.e5. [PMID: 33400917 DOI: 10.1016/j.str.2020.12.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 09/28/2020] [Accepted: 12/08/2020] [Indexed: 10/22/2022]
Abstract
The majority of eukaryotic proteins is modified by N-terminal acetylation, which plays a fundamental role in protein homeostasis, localization, and complex formation. N-terminal acetyltransferases (NATs) mainly act co-translationally on newly synthesized proteins at the ribosomal tunnel exit. NatA is the major NAT consisting of Naa10 catalytic and Naa15 auxiliary subunits, and with Naa50 forms the NatE complex. Naa50 has recently been identified in Arabidopsis thaliana and is important for plant development and stress response regulation. Here, we determined high-resolution X-ray crystal structures of AtNaa50 in complex with AcCoA and a bisubstrate analog. We characterized its substrate specificity, determined its enzymatic parameters, and identified functionally important residues. Even though Naa50 is conserved among species, we highlight differences between Arabidopsis and yeast, where Naa50 is catalytically inactive but binds CoA conjugates. Our study provides insights into Naa50 conservation, species-specific adaptations, and serves as a basis for further studies of NATs in plants.
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Affiliation(s)
| | - Jürgen Kopp
- Heidelberg University Biochemistry Center, 69120 Heidelberg, Germany
| | - Laura Armbruster
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Markus Wirtz
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Karine Lapouge
- Heidelberg University Biochemistry Center, 69120 Heidelberg, Germany
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center, 69120 Heidelberg, Germany.
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18
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Monteuuis G, Miścicka A, Świrski M, Zenad L, Niemitalo O, Wrobel L, Alam J, Chacinska A, Kastaniotis AJ, Kufel J. Non-canonical translation initiation in yeast generates a cryptic pool of mitochondrial proteins. Nucleic Acids Res 2019; 47:5777-5791. [PMID: 31216041 PMCID: PMC6582344 DOI: 10.1093/nar/gkz301] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 04/12/2019] [Accepted: 04/16/2019] [Indexed: 12/15/2022] Open
Abstract
Utilization of non-AUG alternative translation start sites is most common in bacteria and viruses, but it has been also reported in other organisms. This phenomenon increases proteome complexity by allowing expression of multiple protein isoforms from a single gene. In Saccharomyces cerevisiae, a few described cases concern proteins that are translated from upstream near-cognate start codons as N-terminally extended variants that localize to mitochondria. Using bioinformatics tools, we provide compelling evidence that in yeast the potential for producing alternative protein isoforms by non-AUG translation initiation is much more prevalent than previously anticipated and may apply to as many as a few thousand proteins. Several hundreds of candidates are predicted to gain a mitochondrial targeting signal (MTS), generating an unrecognized pool of mitochondrial proteins. We confirmed mitochondrial localization of a subset of proteins previously not identified as mitochondrial, whose standard forms do not carry an MTS. Our data highlight the potential of non-canonical translation initiation in expanding the capacity of the mitochondrial proteome and possibly also other cellular features.
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Affiliation(s)
- Geoffray Monteuuis
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O. Box 5400, FIN-90014 Finland
| | - Anna Miścicka
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
| | - Michał Świrski
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
| | - Lounis Zenad
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
| | - Olli Niemitalo
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O. Box 5400, FIN-90014 Finland
| | - Lidia Wrobel
- International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
| | - Jahangir Alam
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O. Box 5400, FIN-90014 Finland
| | - Agnieszka Chacinska
- International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland.,Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Alexander J Kastaniotis
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O. Box 5400, FIN-90014 Finland
| | - Joanna Kufel
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
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19
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Cheng H, Gottlieb L, Marchi E, Kleyner R, Bhardwaj P, Rope AF, Rosenheck S, Moutton S, Philippe C, Eyaid W, Alkuraya FS, Toribio J, Mena R, Prada CE, Stessman H, Bernier R, Wermuth M, Kauffmann B, Blaumeiser B, Kooy RF, Baralle D, Mancini GMS, Conway SJ, Xia F, Chen Z, Meng L, Mihajlovic L, Marmorstein R, Lyon GJ. Phenotypic and biochemical analysis of an international cohort of individuals with variants in NAA10 and NAA15. Hum Mol Genet 2019; 28:2900-2919. [PMID: 31127942 PMCID: PMC6736318 DOI: 10.1093/hmg/ddz111] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 04/29/2019] [Accepted: 05/20/2019] [Indexed: 11/13/2022] Open
Abstract
N-alpha-acetylation is one of the most common co-translational protein modifications in humans and is essential for normal cell function. NAA10 encodes for the enzyme NAA10, which is the catalytic subunit in the N-terminal acetyltransferase A (NatA) complex. The auxiliary and regulatory subunits of the NatA complex are NAA15 and Huntington-interacting protein (HYPK), respectively. Through a genotype-first approach with exome sequencing, we identified and phenotypically characterized 30 individuals from 30 unrelated families with 17 different de novo or inherited, dominantly acting missense variants in NAA10 or NAA15. Clinical features of affected individuals include variable levels of intellectual disability, delayed speech and motor milestones and autism spectrum disorder. Additionally, some subjects present with mild craniofacial dysmorphology, congenital cardiac anomalies and seizures. One of the individuals is an 11-year-old boy with a frameshift variant in exon 7 of NAA10, who presents most notably with microphthalmia, which confirms a prior finding with a single family with Lenz microphthalmia syndrome. Biochemical analyses of variants as part of the human NatA complex, as well as enzymatic analyses with and without the HYPK regulatory subunit, help to explain some of the phenotypic differences seen among the different variants.
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Affiliation(s)
- Hanyin Cheng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Leah Gottlieb
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Elaine Marchi
- Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY 10314, USA
| | - Robert Kleyner
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Puja Bhardwaj
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Alan F Rope
- Kaiser Permanente Center for Health Research, Portland, OR 97227, USA
- Genome Medical, South San Francisco, CA 94080, USA
| | - Sarah Rosenheck
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Sébastien Moutton
- Reference Center for Developmental Anomalies, Department of Medical Genetics, Dijon University Hospital, Dijon, France
- Génétique des Anomalies du développement, INSERM U1231, Lipides Nutrition et Cancer, UMR1231, Université de Bourgogne, F-21000, Dijon 21070, France
| | - Christophe Philippe
- Génétique des Anomalies du développement, INSERM U1231, Lipides Nutrition et Cancer, UMR1231, Université de Bourgogne, F-21000, Dijon 21070, France
- Laboratoire de Génétique, Innovation Diagnostic Génomique des Maladies Rares UF6254, Plate-forme de Biologie Hospitalo-Universitaire, Centre Hospitalier Universitaire, Dijon 21070, France
| | - Wafaa Eyaid
- King Abdulaziz Medical City, King Saud Bin AbdulAziz University—Health Science, King Abdullah International Medical Research Center, Riyadh 11426, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
- Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
| | - Janet Toribio
- Division of Cardiology, CEDIMAT, Santo Domingo 51000, Dominican Republic
| | - Rafael Mena
- Neonatal Intensive Care Unit, Centro de Obstetricia y Ginecologia, Santo Domingo, Dominican Republic
- Division Of Neonatology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Carlos E Prada
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Holly Stessman
- Department of Pharmacology, Creighton University Medical School, Omaha, NE 68178, USA
| | - Raphael Bernier
- Department of Psychiatry, University of Washington, Seattle, WA 98195, USA
| | - Marieke Wermuth
- Klinik für Kinder-und Jugendmedizin, Neuropädiatrie, Klinikum Links der Weser, Senator-Weβling-Str.1. in 28211 Bremen, Germany
| | - Birgit Kauffmann
- Klinik für Kinder-und Jugendmedizin, Neuropädiatrie, Klinikum Links der Weser, Senator-Weβling-Str.1. in 28211 Bremen, Germany
| | | | - R Frank Kooy
- Department of Medical Genetics, University of Antwerp, Antwerp 2000, Belgium
| | - Diana Baralle
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton SO16 5YA, UK
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, UK
| | - Grazia M S Mancini
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam 3015 GD, The Netherlands
| | - Simon J Conway
- HB Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Baylor Genetics, Houston, TX 77021, USA
| | - Zhao Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Baylor Genetics, Houston, TX 77021, USA
| | - Linyan Meng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Baylor Genetics, Houston, TX 77021, USA
| | | | - Ronen Marmorstein
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gholson J Lyon
- Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY 10314, USA
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA
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20
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N-terminal acetylation and methylation differentially affect the function of MYL9. Biochem J 2018; 475:3201-3219. [PMID: 30242065 DOI: 10.1042/bcj20180638] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 09/18/2018] [Accepted: 09/19/2018] [Indexed: 12/30/2022]
Abstract
Deciphering the histone code has illustrated that acetylation or methylation on the same residue can have analogous or opposing roles. However, little is known about the interplay between these post-translational modifications (PTMs) on the same nonhistone residues. We have recently discovered that N-terminal acetyltransferases (NATs) and N-terminal methyltransferases (NRMTs) can have overlapping substrates and identified myosin regulatory light chain 9 (MYL9) as the first confirmed protein to occur in either α-amino-methylated (Nα-methyl) or α-amino-acetylated (Nα-acetyl) states in vivo Here we aim to determine if these PTMs function similarly or create different MYL9 proteoforms with distinct roles. We use enzymatic assays to directly verify MYL9 is a substrate of both NRMT1 and NatA and generate mutants of MYL9 that are exclusive for Nα-acetylation or Nα-methylation. We then employ eukaryotic cell models to probe the regulatory functions of these Nα-PTMs on MYL9. Our results show that, contrary to prevailing dogma, neither of these modifications regulate the stability of MYL9. Rather, exclusive Nα-acetylation promotes cytoplasmic roles of MYL9, while exclusive Nα-methylation promotes the nuclear role of MYL9 as a transcription factor. The increased cytoplasmic activity of Nα-acetylated MYL9 corresponds with increased phosphorylation at serine 19, a key MYL9 activating PTM. Increased nuclear activity of Nα-methylated MYL9 corresponds with increased DNA binding. Nα-methylation also results in a decrease of interactions between the N-terminus of MYL9 and a host of cytoskeletal proteins. These results confirm that Nα-acetylation and Nα-methylation differentially affect MYL9 function by creating distinct proteoforms with different internal PTM patterns and binding properties.
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21
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Varland S, Aksnes H, Kryuchkov F, Impens F, Van Haver D, Jonckheere V, Ziegler M, Gevaert K, Van Damme P, Arnesen T. N-terminal Acetylation Levels Are Maintained During Acetyl-CoA Deficiency in Saccharomyces cerevisiae. Mol Cell Proteomics 2018; 17:2309-2323. [PMID: 30150368 PMCID: PMC6283290 DOI: 10.1074/mcp.ra118.000982] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 08/22/2018] [Indexed: 12/17/2022] Open
Abstract
Nt-acetylation is a prevalent protein modification catalyzed by N-terminal acetyltransferases using acetyl-CoA as acetyl donor. Here, we performed a global analysis of Nt-acetylation in yeast following nutrient starvation. Contrary to histone acetylation, which is sensitive to acetyl-CoA levels, we demonstrate that Nt-acetylation remains largely unaffected to changes in cellular metabolism. We did, however, identify two protein groups that were differentially Nt-acetylated, one showing the same sensitivity to acetyl-CoA as histones. We propose that specific, rather than global, Nt-acetylation events are subject to metabolic regulation. N-terminal acetylation (Nt-acetylation) is a highly abundant protein modification in eukaryotes and impacts a wide range of cellular processes, including protein quality control and stress tolerance. Despite its prevalence, the mechanisms regulating Nt-acetylation are still nebulous. Here, we present the first global study of Nt-acetylation in yeast cells as they progress to stationary phase in response to nutrient starvation. Surprisingly, we found that yeast cells maintain their global Nt-acetylation levels upon nutrient depletion, despite a marked decrease in acetyl-CoA levels. We further observed two distinct sets of protein N termini that display differential and opposing Nt-acetylation behavior upon nutrient starvation, indicating a dynamic process. The first protein cluster was enriched for annotated N termini showing increased Nt-acetylation in stationary phase compared with exponential growth phase. The second protein cluster was conversely enriched for alternative nonannotated N termini (i.e. N termini indicative of shorter N-terminal proteoforms) and, like histones, showed reduced acetylation levels in stationary phase when acetyl-CoA levels were low. Notably, the degree of Nt-acetylation of Pcl8, a negative regulator of glycogen biosynthesis and two components of the pre-ribosome complex (Rsa3 and Rpl7a) increased during starvation. Moreover, the steady-state levels of these proteins were regulated both by starvation and NatA activity. In summary, this study represents the first comprehensive analysis of metabolic regulation of Nt-acetylation and reveals that specific, rather than global, Nt-acetylation events are subject to metabolic regulation.
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Affiliation(s)
- Sylvia Varland
- Department of Biomedicine, University of Bergen, N-5020 Bergen, Norway; Department of Biological Sciences, University of Bergen, N-5020 Bergen, Norway; Donnelly Center for Cellular and Bio‡molecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada.
| | - Henriette Aksnes
- Department of Biomedicine, University of Bergen, N-5020 Bergen, Norway; Department of Biological Sciences, University of Bergen, N-5020 Bergen, Norway
| | - Fedor Kryuchkov
- Department of Biomedicine, University of Bergen, N-5020 Bergen, Norway
| | - Francis Impens
- VIB-UGent Center for Medical Biotechnology, B-9000 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium; VIB Proteomics Core, B-9000 Ghent, Belgium
| | - Delphi Van Haver
- VIB-UGent Center for Medical Biotechnology, B-9000 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium; VIB Proteomics Core, B-9000 Ghent, Belgium
| | - Veronique Jonckheere
- VIB-UGent Center for Medical Biotechnology, B-9000 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium
| | - Mathias Ziegler
- Department of Biomedicine, University of Bergen, N-5020 Bergen, Norway; Department of Biological Sciences, University of Bergen, N-5020 Bergen, Norway
| | - Kris Gevaert
- VIB-UGent Center for Medical Biotechnology, B-9000 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium
| | - Petra Van Damme
- Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium.
| | - Thomas Arnesen
- Department of Biomedicine, University of Bergen, N-5020 Bergen, Norway; Department of Biological Sciences, University of Bergen, N-5020 Bergen, Norway; Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway
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22
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Lee MN, Kweon HY, Oh GT. N-α-acetyltransferase 10 (NAA10) in development: the role of NAA10. Exp Mol Med 2018; 50:1-11. [PMID: 30054454 PMCID: PMC6063908 DOI: 10.1038/s12276-018-0105-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 04/11/2018] [Indexed: 01/07/2023] Open
Abstract
N-α-acetyltransferase 10 (NAA10) is a subunit of Nα-terminal protein acetyltransferase that plays a role in many biological processes. Among the six N-α-acetyltransferases (NATs) in eukaryotes, the biological significance of the N-terminal acetyl-activity of Naa10 has been the most studied. Recent findings in a few species, including humans, indicate that loss of N-terminal acetylation by NAA10 is associated with developmental defects. However, very little is known about the role of NAA10, and more research is required in relation to the developmental process. This review summarizes recent studies to understand the function of NAA10 in the development of multicellular organisms. Further investigations are needed into the role of a key enzyme in biological development and its encoding gene. The enzyme N-α-acetyltransferase 10 (NAA10), encoded by the NAA10 gene, plays a role in multiple biological processes. While the function of NAA10 has been studied in cancer, less is known about the roles of the gene and the enzyme during development, according to a review by Goo Taeg Oh and co-workers at the Ewha Womans University in Seoul, South Korea. Mutations in NAA10 are found in patients with developmental delay, cardiac problems and skeletal abnormalities, while reduced enzyme activity is associated with developmental defects. Mouse studies suggest a role for NAA10 in neuronal development, bone formation and healthy sperm generation. The impact of variable NAA10 expression in different organs at different developmental stages needs clarification.
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Affiliation(s)
- Mi-Ni Lee
- Immune and Vascular Cell Network Research Center, National Creative Initiatives, Department of Life Sciences, Ewha Womans University, Seoul, Republic of Korea
| | - Hyae Yon Kweon
- Immune and Vascular Cell Network Research Center, National Creative Initiatives, Department of Life Sciences, Ewha Womans University, Seoul, Republic of Korea
| | - Goo Taeg Oh
- Immune and Vascular Cell Network Research Center, National Creative Initiatives, Department of Life Sciences, Ewha Womans University, Seoul, Republic of Korea.
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23
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Lee D, Jang MK, Seo JH, Ryu SH, Kim JA, Chung YH. ARD1/NAA10 in hepatocellular carcinoma: pathways and clinical implications. Exp Mol Med 2018; 50:1-12. [PMID: 30054466 PMCID: PMC6063946 DOI: 10.1038/s12276-018-0106-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 04/11/2018] [Indexed: 12/21/2022] Open
Abstract
Hepatocellular carcinoma (HCC), a representative example of a malignancy with a poor prognosis, is characterized by high mortality because it is typically in an advanced stage at diagnosis and leaves very little hepatic functional reserve. Despite advances in medical and surgical techniques, there is no omnipotent tool that can diagnose HCC early and then cure it medically or surgically. Several recent studies have shown that a variety of pathways are involved in the development, growth, and even metastasis of HCC. Among a variety of cytokines or molecules, some investigators have suggested that arrest-defective 1 (ARD1), an acetyltransferase, plays a key role in the development of malignancies. Although ARD1 is thought to be centrally involved in the cell cycle, cell migration, apoptosis, differentiation, and proliferation, the role of ARD1 and its potential mechanistic involvement in HCC remain unclear. Here, we review the present literature on ARD1. First, we provide an overview of the essential structure, functions, and molecular mechanisms or pathways of ARD1 in HCC. Next, we discuss potential clinical implications and perspectives. We hope that, by providing new insights into ARD1, this review will help to guide the next steps in the development of markers for the early detection and prognosis of HCC. A protein that is highly expressed in cancer with extensive blood vessel development may provide a potential biomarker for early-stage liver cancer. Liver cancer is often not diagnosed until it is advanced and is also hard to be cured despite of advances in treatment, meaning patients often die from the disease. No tools for early detection or prognosis prediction exist, and scientists are keen to find useful biomarker molecules. Young-Hwa Chung at the University of Ulsan College of Medicine, Asan Medical Center, Seoul, and co-workers in South Korea reviewed recent research into one possible cancer-related protein, arrest-defective 1 (ARD1), known to be highly expressed in certain cancers and possibly associated with poor prognosis. While ARD1 appears to regulate pathways critical to cancer progression and promote cancer cell invasiveness, further in-depth investigations are needed to clarify its specific role in liver cancer.
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Affiliation(s)
- Danbi Lee
- Department of Internal Medicine, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Republic of Korea
| | - Myoung-Kuk Jang
- Department of Internal Medicine, Hallym University College of Medicine, Kangdong Sacred Heart Hospital, Seoul, Republic of Korea
| | - Ji Hae Seo
- Department of Biochemistry, Keimyung University School of Medicine, Daegu, Republic of Korea
| | - Soo Hyung Ryu
- Department of Internal Medicine, Inje University College of Medicine, Seoul Paik Hospital, Seoul, Republic of Korea
| | | | - Young-Hwa Chung
- Department of Internal Medicine, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Republic of Korea.
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24
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A novel NAA10 variant with impaired acetyltransferase activity causes developmental delay, intellectual disability, and hypertrophic cardiomyopathy. Eur J Hum Genet 2018; 26:1294-1305. [PMID: 29748569 DOI: 10.1038/s41431-018-0136-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 02/24/2018] [Accepted: 03/02/2018] [Indexed: 11/09/2022] Open
Abstract
The NAA10-NAA15 complex (NatA) is an N-terminal acetyltransferase that catalyzes N-terminal acetylation of ~40% of all human proteins. N-terminal acetylation has several different roles in the cell, including altering protein stability and degradation, protein localization and protein-protein interactions. In recent years several X-linked NAA10 variants have been associated with genetic disorders. We have identified a previously undescribed NAA10 c.215T>C p.(Ile72Thr) variant in three boys from two unrelated families with a milder phenotypic spectrum in comparison to most of the previously described patients with NAA10 variants. These boys have development delay, intellectual disability, and cardiac abnormalities as overlapping phenotypes. Functional studies reveal that NAA10 Ile72Thr is destabilized, while binding to NAA15 most likely is intact. Surprisingly, the NatA activity of NAA10 Ile72Thr appears normal while its monomeric activity is decreased. This study further broadens the phenotypic spectrum associated with NAA10 deficiency, and adds to the evidence that genotype-phenotype correlations for NAA10 variants are much more complex than initially anticipated.
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25
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Gottlieb L, Marmorstein R. Structure of Human NatA and Its Regulation by the Huntingtin Interacting Protein HYPK. Structure 2018; 26:925-935.e8. [PMID: 29754825 DOI: 10.1016/j.str.2018.04.003] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 03/22/2018] [Accepted: 04/05/2018] [Indexed: 12/31/2022]
Abstract
Co-translational N-terminal protein acetylation regulates many protein functions including degradation, folding, interprotein interactions, and targeting. Human NatA (hNatA), one of six conserved metazoan N-terminal acetyltransferases, contains Naa10 catalytic and Naa15 auxiliary subunits, and associates with the intrinsically disordered Huntingtin yeast two-hybrid protein K (HYPK). We report on the crystal structures of hNatA and hNatA/HYPK, and associated biochemical and enzymatic analyses. We demonstrate that hNatA contains unique features: a stabilizing inositol hexaphosphate (IP6) molecule and a metazoan-specific Naa15 domain that mediates high-affinity HYPK binding. We find that HYPK harbors intrinsic hNatA-specific inhibitory activity through a bipartite structure: a ubiquitin-associated domain that binds a hNaa15 metazoan-specific region and an N-terminal loop-helix region that distorts the hNaa10 active site. We show that HYPK binding blocks hNaa50 targeting to hNatA, likely limiting Naa50 ribosome localization in vivo. These studies provide a model for metazoan NAT activity and HYPK regulation of N-terminal acetylation.
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Affiliation(s)
- Leah Gottlieb
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Ronen Marmorstein
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biochemistry and Biophysics, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104, USA.
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26
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Cheng H, Dharmadhikari AV, Varland S, Ma N, Domingo D, Kleyner R, Rope AF, Yoon M, Stray-Pedersen A, Posey JE, Crews SR, Eldomery MK, Akdemir ZC, Lewis AM, Sutton VR, Rosenfeld JA, Conboy E, Agre K, Xia F, Walkiewicz M, Longoni M, High FA, van Slegtenhorst MA, Mancini GMS, Finnila CR, van Haeringen A, den Hollander N, Ruivenkamp C, Naidu S, Mahida S, Palmer EE, Murray L, Lim D, Jayakar P, Parker MJ, Giusto S, Stracuzzi E, Romano C, Beighley JS, Bernier RA, Küry S, Nizon M, Corbett MA, Shaw M, Gardner A, Barnett C, Armstrong R, Kassahn KS, Van Dijck A, Vandeweyer G, Kleefstra T, Schieving J, Jongmans MJ, de Vries BBA, Pfundt R, Kerr B, Rojas SK, Boycott KM, Person R, Willaert R, Eichler EE, Kooy RF, Yang Y, Wu JC, Lupski JR, Arnesen T, Cooper GM, Chung WK, Gecz J, Stessman HAF, Meng L, Lyon GJ. Truncating Variants in NAA15 Are Associated with Variable Levels of Intellectual Disability, Autism Spectrum Disorder, and Congenital Anomalies. Am J Hum Genet 2018; 102:985-994. [PMID: 29656860 DOI: 10.1016/j.ajhg.2018.03.004] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 02/27/2018] [Indexed: 11/30/2022] Open
Abstract
N-alpha-acetylation is a common co-translational protein modification that is essential for normal cell function in humans. We previously identified the genetic basis of an X-linked infantile lethal Mendelian disorder involving a c.109T>C (p.Ser37Pro) missense variant in NAA10, which encodes the catalytic subunit of the N-terminal acetyltransferase A (NatA) complex. The auxiliary subunit of the NatA complex, NAA15, is the dimeric binding partner for NAA10. Through a genotype-first approach with whole-exome or genome sequencing (WES/WGS) and targeted sequencing analysis, we identified and phenotypically characterized 38 individuals from 33 unrelated families with 25 different de novo or inherited, dominantly acting likely gene disrupting (LGD) variants in NAA15. Clinical features of affected individuals with LGD variants in NAA15 include variable levels of intellectual disability, delayed speech and motor milestones, and autism spectrum disorder. Additionally, mild craniofacial dysmorphology, congenital cardiac anomalies, and seizures are present in some subjects. RNA analysis in cell lines from two individuals showed degradation of the transcripts with LGD variants, probably as a result of nonsense-mediated decay. Functional assays in yeast confirmed a deleterious effect for two of the LGD variants in NAA15. Further supporting a mechanism of haploinsufficiency, individuals with copy-number variant (CNV) deletions involving NAA15 and surrounding genes can present with mild intellectual disability, mild dysmorphic features, motor delays, and decreased growth. We propose that defects in NatA-mediated N-terminal acetylation (NTA) lead to variable levels of neurodevelopmental disorders in humans, supporting the importance of the NatA complex in normal human development.
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Affiliation(s)
| | | | - Sylvia Varland
- Department of Biomedicine, University of Bergen, N-5020 Bergen, Norway; Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway
| | - Ning Ma
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Division of Cardiology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Deepti Domingo
- School of Biological Sciences, Faculty of Genes and Evolution, the University of Adelaide, Adelaide, SA 5000, Australia
| | - Robert Kleyner
- Stanley Institute for Cognitive Genomics, 1Bungtown Road, Cold Spring Harbor Laboratory, NY 11724, USA
| | - Alan F Rope
- Department of Medical Genetics, Kaiser Permanente Northwest, Portland, OR 97227, USA
| | - Margaret Yoon
- Stanley Institute for Cognitive Genomics, 1Bungtown Road, Cold Spring Harbor Laboratory, NY 11724, USA
| | - Asbjørg Stray-Pedersen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Norwegian National Unit for Newborn Screening, Division of Pediatric and Adolescent Medicine, Oslo University Hospital, N-0424 Oslo, and Institute of Clinical Medicine, University of Oslo, N-0318 Oslo, Norway
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sarah R Crews
- Department of Pharmacology, Creighton University Medical School, Omaha, NE, 68178, USA
| | - Mohammad K Eldomery
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zeynep Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Andrea M Lewis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Texas Children's Hospital and Baylor College of Medicine, Houston, TX 77030, USA
| | - Vernon R Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Erin Conboy
- Department of Clinical Genomics, Mayo Clinic, MN 55905, USA
| | - Katherine Agre
- Department of Clinical Genomics, Mayo Clinic, MN 55905, USA
| | - Fan Xia
- Baylor Genetics, Houston, TX, 77021, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Magdalena Walkiewicz
- Baylor Genetics, Houston, TX, 77021, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; The National Institute of Allergy and Infectious Disease, The National Institutes of Health, Bethesda, MD 20892, USA
| | - Mauro Longoni
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Surgery, Harvard Medical School, Boston, MA 02114, USA
| | - Frances A High
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Pediatrics, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Surgery, Boston Children's Hospital, Boston, MA 02115, USA
| | - Marjon A van Slegtenhorst
- Department of Clinical Genetics, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands
| | - Grazia M S Mancini
- Department of Clinical Genetics, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands
| | | | - Arie van Haeringen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, 2333, The Netherlands
| | - Nicolette den Hollander
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, 2333, The Netherlands
| | - Claudia Ruivenkamp
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, 2333, The Netherlands
| | - Sakkubai Naidu
- Kennedy Krieger Institute, 801 North Broadway Baltimore, MD 21205, USA
| | - Sonal Mahida
- Kennedy Krieger Institute, 801 North Broadway Baltimore, MD 21205, USA
| | - Elizabeth E Palmer
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, NSW 2298, Australia; School of Women's and Children's Health, University of New South Wales, Sydney, NSW 2031, Australia
| | - Lucinda Murray
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, NSW 2298, Australia
| | - Derek Lim
- West Midlands Regional Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Mindelsohn Way, Birmingham B15 2TG, UK
| | - Parul Jayakar
- Division of Genetics and Metabolism, Nicklaus Children's Hospital, Miami, FL 33155, USA
| | - Michael J Parker
- Sheffield Clinical Genetics Service, Sheffield Children's Hospital, Western Bank, Sheffield S10 2TH, UK
| | - Stefania Giusto
- Oasi Research Institute - Istituto di Ricovero e Cura a Carattere Scientifico, Troina 94018, Italy
| | - Emanuela Stracuzzi
- Oasi Research Institute - Istituto di Ricovero e Cura a Carattere Scientifico, Troina 94018, Italy
| | - Corrado Romano
- Oasi Research Institute - Istituto di Ricovero e Cura a Carattere Scientifico, Troina 94018, Italy
| | | | - Raphael A Bernier
- Department of Psychiatry, University of Washington, Seattle WA, 98195, USA
| | - Sébastien Küry
- Department of Medical Genetics, Centre Hospitalier Universitaire, Nantes 44093, France
| | - Mathilde Nizon
- Department of Medical Genetics, Centre Hospitalier Universitaire, Nantes 44093, France
| | - Mark A Corbett
- Adelaide Medical School and Robinson Research Institute, the University of Adelaide, Adelaide, SA 5000, Australia
| | - Marie Shaw
- Adelaide Medical School and Robinson Research Institute, the University of Adelaide, Adelaide, SA 5000, Australia
| | - Alison Gardner
- Adelaide Medical School and Robinson Research Institute, the University of Adelaide, Adelaide, SA 5000, Australia
| | - Christopher Barnett
- Paediatric and Reproductive Genetics, South Australian Clinical Genetics Service, SA Pathology (at Women's and Children's Hospital), Adelaide, SA 5006, Australia
| | - Ruth Armstrong
- East Anglian Medical Genetics Service, Clinical Genetics, Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Karin S Kassahn
- Department of Genetics and Molecular Pathology, SA Pathology, Women's and Children's Hospital, North Adelaide, SA 5006, Australia; School of Biological Sciences, University of Adelaide, Adelaide, SA 5000, Australia
| | - Anke Van Dijck
- Department of Medical Genetics, University of Antwerp, Antwerp 2000, Belgium
| | - Geert Vandeweyer
- Department of Medical Genetics, University of Antwerp, Antwerp 2000, Belgium
| | - Tjitske Kleefstra
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500HB, The Netherlands
| | - Jolanda Schieving
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500HB, The Netherlands
| | - Marjolijn J Jongmans
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500HB, The Netherlands
| | - Bert B A de Vries
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500HB, The Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500HB, The Netherlands
| | - Bronwyn Kerr
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester M13 9PL, UK; Division of Evolution and Genomic Sciences School of Biological Sciences, University of Manchester, Manchester M13 9PL, UK
| | - Samantha K Rojas
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | | | | | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - R Frank Kooy
- Department of Medical Genetics, University of Antwerp, Antwerp 2000, Belgium
| | - Yaping Yang
- Baylor Genetics, Houston, TX, 77021, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Joseph C Wu
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Division of Cardiology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center of Baylor College of Medicine, Houston, TX 77030, USA
| | - Thomas Arnesen
- Department of Biomedicine, University of Bergen, N-5020 Bergen, Norway; Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway; Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway
| | - Gregory M Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Jozef Gecz
- School of Biological Sciences, Faculty of Genes and Evolution, the University of Adelaide, Adelaide, SA 5000, Australia; Adelaide Medical School and Robinson Research Institute, the University of Adelaide, Adelaide, SA 5000, Australia; Healthy Mothers, Babies and Children, South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia
| | - Holly A F Stessman
- Department of Pharmacology, Creighton University Medical School, Omaha, NE, 68178, USA
| | - Linyan Meng
- Baylor Genetics, Houston, TX, 77021, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Gholson J Lyon
- Stanley Institute for Cognitive Genomics, 1Bungtown Road, Cold Spring Harbor Laboratory, NY 11724, USA.
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27
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McTiernan N, Støve SI, Aukrust I, Mårli MT, Myklebust LM, Houge G, Arnesen T. NAA10 dysfunction with normal NatA-complex activity in a girl with non-syndromic ID and a de novo NAA10 p.(V111G) variant - a case report. BMC MEDICAL GENETICS 2018; 19:47. [PMID: 29558889 PMCID: PMC5859388 DOI: 10.1186/s12881-018-0559-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 03/09/2018] [Indexed: 01/02/2023]
Abstract
Background The NAA10-NAA15 (NatA) protein complex is an N-terminal acetyltransferase responsible for acetylating ~ 40% of eukaryotic proteins. In recent years, NAA10 variants have been found in patients with an X-linked developmental disorder called Ogden syndrome in its most severe form and, in other familial or de novo cases, with variable degrees of syndromic intellectual disability (ID) affecting both sexes. Case presentation Here we report and functionally characterize a novel and de novo NAA10 (NM_003491.3) c.332 T > G p.(V111G) missense variant, that was detected by trio-based whole exome sequencing in an 11 year old girl with mild/moderate non-syndromic intellectual disability. She had delayed motor and language development, but normal behavior without autistic traits. Her blood leukocyte X-inactivation pattern was within normal range (80/20). Functional characterization of NAA10-V111G by cycloheximide chase experiments suggests that NAA10-V111G has a reduced stability compared to NAA10-WT, and in vitro acetylation assays revealed a reduced enzymatic activity of monomeric NAA10-V111G but not for NAA10-V111G in complex with NAA15 (NatA enzymatic activity). Conclusions We show that NAA10-V111G has a reduced stability and monomeric catalytic activity, while NatA function remains unaltered. This is the first example of isolated NAA10 dysfunction in a case of ID, suggesting that the syndromic cases may also require a degree of compromised NatA function.
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Affiliation(s)
- Nina McTiernan
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Svein Isungset Støve
- Department of Biological Sciences, University of Bergen, Bergen, Norway.,Department of Biomedicine, University of Bergen, Jonas Lies vei 91, N-5020, Bergen, Norway
| | - Ingvild Aukrust
- Department of Medical Genetics, Haukeland University Hospital, N-5021, Bergen, Norway
| | | | - Line M Myklebust
- Department of Biological Sciences, University of Bergen, Bergen, Norway.,Department of Biomedicine, University of Bergen, Jonas Lies vei 91, N-5020, Bergen, Norway
| | - Gunnar Houge
- Department of Medical Genetics, Haukeland University Hospital, N-5021, Bergen, Norway.
| | - Thomas Arnesen
- Department of Biological Sciences, University of Bergen, Bergen, Norway. .,Department of Biomedicine, University of Bergen, Jonas Lies vei 91, N-5020, Bergen, Norway. .,Department of Surgery, Haukeland University Hospital, Bergen, Norway.
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28
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Dörfel MJ, Fang H, Crain J, Klingener M, Weiser J, Lyon GJ. Proteomic and genomic characterization of a yeast model for Ogden syndrome. Yeast 2017; 34:19-37. [PMID: 27668839 PMCID: PMC5248646 DOI: 10.1002/yea.3211] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 09/12/2016] [Accepted: 09/16/2016] [Indexed: 11/10/2022] Open
Abstract
Naa10 is an Nα -terminal acetyltransferase that, in a complex with its auxiliary subunit Naa15, co-translationally acetylates the α-amino group of newly synthetized proteins as they emerge from the ribosome. Roughly 40-50% of the human proteome is acetylated by Naa10, rendering this an enzyme one of the most broad substrate ranges known. Recently, we reported an X-linked disorder of infancy, Ogden syndrome, in two families harbouring a c.109 T > C (p.Ser37Pro) variant in NAA10. In the present study we performed in-depth characterization of a yeast model of Ogden syndrome. Stress tests and proteomic analyses suggest that the S37P mutation disrupts Naa10 function and reduces cellular fitness during heat shock, possibly owing to dysregulation of chaperone expression and accumulation. Microarray and RNA-seq revealed a pseudo-diploid gene expression profile in ΔNaa10 cells, probably responsible for a mating defect. In conclusion, the data presented here further support the disruptive nature of the S37P/Ogden mutation and identify affected cellular processes potentially contributing to the severe phenotype seen in Ogden syndrome. Data are available via GEO under identifier GSE86482 or with ProteomeXchange under identifier PXD004923. © 2016 The Authors. Yeast published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Max J. Dörfel
- Stanley Institute for Cognitive Genomics, One Bungtown RoadCold Spring Harbor LaboratoryCold Spring HarborNYUSA
| | - Han Fang
- Stanley Institute for Cognitive Genomics, One Bungtown RoadCold Spring Harbor LaboratoryCold Spring HarborNYUSA
| | - Jonathan Crain
- Stanley Institute for Cognitive Genomics, One Bungtown RoadCold Spring Harbor LaboratoryCold Spring HarborNYUSA
| | - Michael Klingener
- Stanley Institute for Cognitive Genomics, One Bungtown RoadCold Spring Harbor LaboratoryCold Spring HarborNYUSA
| | - Jake Weiser
- Stanley Institute for Cognitive Genomics, One Bungtown RoadCold Spring Harbor LaboratoryCold Spring HarborNYUSA
| | - Gholson J. Lyon
- Stanley Institute for Cognitive Genomics, One Bungtown RoadCold Spring Harbor LaboratoryCold Spring HarborNYUSA
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29
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Goossens J, De Geyter N, Walton A, Eeckhout D, Mertens J, Pollier J, Fiallos-Jurado J, De Keyser A, De Clercq R, Van Leene J, Gevaert K, De Jaeger G, Goormachtig S, Goossens A. Isolation of protein complexes from the model legume Medicago truncatula by tandem affinity purification in hairy root cultures. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:476-489. [PMID: 27377668 DOI: 10.1111/tpj.13258] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 06/21/2016] [Accepted: 06/30/2016] [Indexed: 05/26/2023]
Abstract
Tandem affinity purification coupled to mass spectrometry (TAP-MS) is one of the most powerful techniques to isolate protein complexes and elucidate protein interaction networks. Here, we describe the development of a TAP-MS strategy for the model legume Medicago truncatula, which is widely studied for its ability to produce valuable natural products and to engage in endosymbiotic interactions. As biological material, transgenic hairy roots, generated through Agrobacterium rhizogenes-mediated transformation of M. truncatula seedlings, were used. As proof of concept, proteins involved in the cell cycle, transcript processing and jasmonate signalling were chosen as bait proteins, resulting in a list of putative interactors, many of which confirm the interologue concept of protein interactions, and which can contribute to biological information about the functioning of these bait proteins in planta. Subsequently, binary protein-protein interactions among baits and preys, and among preys were confirmed by a systematic yeast two-hybrid screen. Together, by establishing a M. truncatula TAP-MS platform, we extended the molecular toolbox of this model species.
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Affiliation(s)
- Jonas Goossens
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Nathan De Geyter
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Alan Walton
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
- Department of Medical Protein Research, VIB, Albert Baertsoenkaai 3, B-9000, Gent, Belgium
- Department of Biochemistry, Ghent University, Albert Baertsoenkaai 3, B-9000, Gent, Belgium
| | - Dominique Eeckhout
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Jan Mertens
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Jacob Pollier
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Jennifer Fiallos-Jurado
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Annick De Keyser
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Rebecca De Clercq
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Jelle Van Leene
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Kris Gevaert
- Department of Medical Protein Research, VIB, Albert Baertsoenkaai 3, B-9000, Gent, Belgium
- Department of Biochemistry, Ghent University, Albert Baertsoenkaai 3, B-9000, Gent, Belgium
| | - Geert De Jaeger
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Sofie Goormachtig
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Alain Goossens
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
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30
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Molina-Serrano D, Schiza V, Demosthenous C, Stavrou E, Oppelt J, Kyriakou D, Liu W, Zisser G, Bergler H, Dang W, Kirmizis A. Loss of Nat4 and its associated histone H4 N-terminal acetylation mediates calorie restriction-induced longevity. EMBO Rep 2016; 17:1829-1843. [PMID: 27799288 PMCID: PMC5167350 DOI: 10.15252/embr.201642540] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 09/21/2016] [Accepted: 09/30/2016] [Indexed: 01/07/2023] Open
Abstract
Changes in histone modifications are an attractive model through which environmental signals, such as diet, could be integrated in the cell for regulating its lifespan. However, evidence linking dietary interventions with specific alterations in histone modifications that subsequently affect lifespan remains elusive. We show here that deletion of histone N‐alpha‐terminal acetyltransferase Nat4 and loss of its associated H4 N‐terminal acetylation (N‐acH4) extend yeast replicative lifespan. Notably, nat4Δ‐induced longevity is epistatic to the effects of calorie restriction (CR). Consistent with this, (i) Nat4 expression is downregulated and the levels of N‐acH4 within chromatin are reduced upon CR, (ii) constitutive expression of Nat4 and maintenance of N‐acH4 levels reduces the extension of lifespan mediated by CR, and (iii) transcriptome analysis indicates that nat4Δ largely mimics the effects of CR, especially in the induction of stress‐response genes. We further show that nicotinamidase Pnc1, which is typically upregulated under CR, is required for nat4Δ‐mediated longevity. Collectively, these findings establish histone N‐acH4 as a regulator of cellular lifespan that links CR to increased stress resistance and longevity.
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Affiliation(s)
| | - Vassia Schiza
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | | | - Emmanouil Stavrou
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Jan Oppelt
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
| | - Dimitris Kyriakou
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Wei Liu
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
| | - Gertrude Zisser
- Institut für Molekulare Biowissenschaften, Karl-Franzens-Universität, Graz, Austria
| | - Helmut Bergler
- Institut für Molekulare Biowissenschaften, Karl-Franzens-Universität, Graz, Austria
| | - Weiwei Dang
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
| | - Antonis Kirmizis
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
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31
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Pavlou D, Kirmizis A. Depletion of histone N-terminal-acetyltransferase Naa40 induces p53-independent apoptosis in colorectal cancer cells via the mitochondrial pathway. Apoptosis 2016; 21:298-311. [PMID: 26666750 PMCID: PMC4746217 DOI: 10.1007/s10495-015-1207-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Protein N-terminal acetylation is an abundant post-translational modification in eukaryotes implicated in various fundamental cellular and biochemical processes. This modification is catalysed by evolutionarily conserved N-terminal acetyltransferases (NATs) whose deregulation has been linked to cancer development and thus, are emerging as useful diagnostic and therapeutic targets. Naa40 is a highly selective NAT that acetylates the amino-termini of histones H4 and H2A and acts as a sensor of cell growth in yeast. In the present study, we examine the role of Naa40 in cancer cell survival. We demonstrate that depletion of Naa40 in HCT116 and HT-29 colorectal cancer cells decreases cell survival by enhancing apoptosis, whereas Naa40 reduction in non-cancerous mouse embryonic fibroblasts has no effect on cell viability. Specifically, Naa40 knockdown in colon cancer cells activates the mitochondrial caspase-9-mediated apoptotic cascade. Consistent with this, we show that caspase-9 activation is required for the induced apoptosis because treatment of cells with an irreversible caspase-9 inhibitor impedes apoptosis when Naa40 is depleted. Furthermore, the effect of Naa40-depletion on cell-death is mediated through a p53-independent mechanism since p53-null HCT116 cells still undergo apoptosis upon reduction of the acetyltransferase. Altogether, these findings reveal an anti-apoptotic role for Naa40 and exhibit its potential as a therapeutic target in colorectal cancers.
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Affiliation(s)
- Demetria Pavlou
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Antonis Kirmizis
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus.
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32
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Microscopy-based Saccharomyces cerevisiae complementation model reveals functional conservation and redundancy of N-terminal acetyltransferases. Sci Rep 2016; 6:31627. [PMID: 27555049 PMCID: PMC4995432 DOI: 10.1038/srep31627] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 07/10/2016] [Indexed: 01/05/2023] Open
Abstract
N-terminal acetylation is a highly abundant protein modification catalyzed by N-terminal acetyltransferases (NATs) NatA-NatG. The Saccharomyces cerevisiae protein Arl3 depends on interaction with Sys1 for its localization to the Golgi and this targeting strictly requires NatC-mediated N-terminal acetylation of Arl3. We utilized the Arl3 acetylation-dependent localization phenotype as a model system for assessing the functional conservation and in vivo redundancy of several human NATs. The catalytic subunit of human NatC, hNaa30 (Mak3), restored Arl3 localization in the absence of yNaa30, but only in the presence of either yeast or human Naa35 subunit (Mak10). In contrast, hNaa35 was not able to replace its yeast orthologue without the co-expression of hNaa30, suggesting co-evolution of the two NatC subunits. The most recently discovered and organellar human NAT, NatF/Naa60, restored the Golgi localization of Arl3 in the absence of yNaa30. Interestingly, this was also true for hNaa60 lacking its membrane-binding domain whereas hNaa50 did not complement NatC function. This in vivo redundancy reflects NatC and NatF´s overlapping in vitro substrate specificities. The yeast model presented here provides a robust and rapid readout of NatC and NatF activity in vivo, and revealed evolutionary conservation of the NatC complex and redundancy between NatC and NatF.
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33
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Aksnes H, Drazic A, Marie M, Arnesen T. First Things First: Vital Protein Marks by N-Terminal Acetyltransferases. Trends Biochem Sci 2016; 41:746-760. [PMID: 27498224 DOI: 10.1016/j.tibs.2016.07.005] [Citation(s) in RCA: 172] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 07/01/2016] [Accepted: 07/08/2016] [Indexed: 11/28/2022]
Abstract
N-terminal (Nt) acetylation is known to be a highly abundant co-translational protein modification, but the recent discovery of Golgi- and chloroplast-resident N-terminal acetyltransferases (NATs) revealed that it can also be added post-translationally. Nt-acetylation may act as a degradation signal in a novel branch of the N-end rule pathway, whose functions include the regulation of human blood pressure. Nt-acetylation also modulates protein interactions, targeting, and folding. In plants, Nt-acetylation plays a role in the control of resistance to drought and in regulation of immune responses. Mutations of specific human NATs that decrease their activity can cause either the lethal Ogden syndrome or severe intellectual disability and cardiovascular defects. In sum, recent advances highlight Nt-acetylation as a key factor in many biological pathways.
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Affiliation(s)
- Henriette Aksnes
- Department of Molecular Biology, University of Bergen, 5020 Bergen, Norway
| | - Adrian Drazic
- Department of Molecular Biology, University of Bergen, 5020 Bergen, Norway
| | - Michaël Marie
- Department of Molecular Biology, University of Bergen, 5020 Bergen, Norway
| | - Thomas Arnesen
- Department of Molecular Biology, University of Bergen, 5020 Bergen, Norway; Department of Surgery, Haukeland University Hospital, 5021 Bergen, Norway.
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34
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Drazic A, Myklebust LM, Ree R, Arnesen T. The world of protein acetylation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1372-401. [PMID: 27296530 DOI: 10.1016/j.bbapap.2016.06.007] [Citation(s) in RCA: 525] [Impact Index Per Article: 65.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 06/04/2016] [Accepted: 06/08/2016] [Indexed: 12/30/2022]
Abstract
Acetylation is one of the major post-translational protein modifications in the cell, with manifold effects on the protein level as well as on the metabolome level. The acetyl group, donated by the metabolite acetyl-coenzyme A, can be co- or post-translationally attached to either the α-amino group of the N-terminus of proteins or to the ε-amino group of lysine residues. These reactions are catalyzed by various N-terminal and lysine acetyltransferases. In case of lysine acetylation, the reaction is enzymatically reversible via tightly regulated and metabolism-dependent mechanisms. The interplay between acetylation and deacetylation is crucial for many important cellular processes. In recent years, our understanding of protein acetylation has increased significantly by global proteomics analyses and in depth functional studies. This review gives a general overview of protein acetylation and the respective acetyltransferases, and focuses on the regulation of metabolic processes and physiological consequences that come along with protein acetylation.
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Affiliation(s)
- Adrian Drazic
- Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway
| | - Line M Myklebust
- Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway
| | - Rasmus Ree
- Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway; Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway
| | - Thomas Arnesen
- Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway; Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway.
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35
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Saunier C, Støve SI, Popp B, Gérard B, Blenski M, AhMew N, de Bie C, Goldenberg P, Isidor B, Keren B, Leheup B, Lampert L, Mignot C, Tezcan K, Mancini GMS, Nava C, Wasserstein M, Bruel AL, Thevenon J, Masurel A, Duffourd Y, Kuentz P, Huet F, Rivière JB, van Slegtenhorst M, Faivre L, Piton A, Reis A, Arnesen T, Thauvin-Robinet C, Zweier C. Expanding the Phenotype Associated with NAA10-Related N-Terminal Acetylation Deficiency. Hum Mutat 2016; 37:755-64. [PMID: 27094817 PMCID: PMC5084832 DOI: 10.1002/humu.23001] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 04/08/2016] [Indexed: 11/10/2022]
Abstract
N-terminal acetylation is a common protein modification in eukaryotes associated with numerous cellular processes. Inherited mutations in NAA10, encoding the catalytic subunit of the major N-terminal acetylation complex NatA have been associated with diverse, syndromic X-linked recessive disorders, whereas de novo missense mutations have been reported in one male and one female individual with severe intellectual disability but otherwise unspecific phenotypes. Thus, the full genetic and clinical spectrum of NAA10 deficiency is yet to be delineated. We identified three different novel and one known missense mutation in NAA10, de novo in 11 females, and due to maternal germ line mosaicism in another girl and her more severely affected and deceased brother. In vitro enzymatic assays for the novel, recurrent mutations p.(Arg83Cys) and p.(Phe128Leu) revealed reduced catalytic activity. X-inactivation was random in five females. The core phenotype of X-linked NAA10-related N-terminal-acetyltransferase deficiency in both males and females includes developmental delay, severe intellectual disability, postnatal growth failure with severe microcephaly, and skeletal or cardiac anomalies. Genotype-phenotype correlations within and between both genders are complex and may include various factors such as location and nature of mutations, enzymatic stability and activity, and X-inactivation in females.
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Affiliation(s)
- Chloé Saunier
- Centre de Référence maladies rares « Anomalies du Développement et syndrome malformatifs » de l'Est et Centre de Génétique, Hôpital d'Enfants, CHU, Dijon, France.,Service de Pédiatrie, Hôpital d'Enfants, CHU Dijon, Dijon, France
| | - Svein Isungset Støve
- Department of Molecular Biology, University of Bergen, Bergen, Norway.,Department of Surgery, Haukeland University Hospital, Bergen, Norway
| | - Bernt Popp
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Bénédicte Gérard
- Laboratoire de Génétique Moléculaire, CHRU Strasbourg, Strasbourg, France
| | - Marina Blenski
- Department of Molecular Biology, University of Bergen, Bergen, Norway
| | - Nicholas AhMew
- Division of Genetics and Metabolism, Children's National Medical Center, Washington DC
| | | | - Paula Goldenberg
- Medical Genetics, Massachusetts General Hospital, Boston, Massachusetts
| | - Bertrand Isidor
- Service de Génétique Médicale, CHU Nantes, Nantes, France.,INSERM, UMR-S 957, Nantes, France
| | - Boris Keren
- AP-HP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, Paris, France.,UPMC, Inserm, CNRS, UM 75, U 1127, UMR 7225, ICM, Paris, F-75013, France
| | - Bruno Leheup
- Service de Génétique Médicale, Hôpital Brabois, CHU Nancy, Nancy, France
| | - Laetitia Lampert
- Service de Génétique Médicale, Hôpital Brabois, CHU Nancy, Nancy, France
| | - Cyril Mignot
- APHP, Département de Génétique et Centre de Référence Déficiences Intellectuelles de Causes Rares, Groupe Hospitalier Pitié Salpêtrière, Paris, France
| | - Kamer Tezcan
- Kaiser Permanente, Department of Genetics, Sacramento, California
| | - Grazia M S Mancini
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Caroline Nava
- AP-HP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, Paris, France.,UPMC, Inserm, CNRS, UM 75, U 1127, UMR 7225, ICM, Paris, F-75013, France
| | - Melissa Wasserstein
- Departments of Genetics and Genomic Sciences and Pediatrics, Icahn School of Medicine at Mount Sinai, New York
| | - Ange-Line Bruel
- FHU-TRANSLAD, Université de Bourgogne/CHU Dijon, Dijon, France.,Equipe EA4271 GAD, Université de Bourgogne, Dijon, France
| | - Julien Thevenon
- Centre de Référence maladies rares « Anomalies du Développement et syndrome malformatifs » de l'Est et Centre de Génétique, Hôpital d'Enfants, CHU, Dijon, France.,FHU-TRANSLAD, Université de Bourgogne/CHU Dijon, Dijon, France.,Equipe EA4271 GAD, Université de Bourgogne, Dijon, France
| | - Alice Masurel
- Centre de Référence maladies rares « Anomalies du Développement et syndrome malformatifs » de l'Est et Centre de Génétique, Hôpital d'Enfants, CHU, Dijon, France.,FHU-TRANSLAD, Université de Bourgogne/CHU Dijon, Dijon, France
| | - Yannis Duffourd
- FHU-TRANSLAD, Université de Bourgogne/CHU Dijon, Dijon, France.,Equipe EA4271 GAD, Université de Bourgogne, Dijon, France
| | - Paul Kuentz
- FHU-TRANSLAD, Université de Bourgogne/CHU Dijon, Dijon, France.,Equipe EA4271 GAD, Université de Bourgogne, Dijon, France
| | - Frédéric Huet
- Service de Pédiatrie, Hôpital d'Enfants, CHU Dijon, Dijon, France.,FHU-TRANSLAD, Université de Bourgogne/CHU Dijon, Dijon, France.,Equipe EA4271 GAD, Université de Bourgogne, Dijon, France
| | - Jean-Baptiste Rivière
- FHU-TRANSLAD, Université de Bourgogne/CHU Dijon, Dijon, France.,Equipe EA4271 GAD, Université de Bourgogne, Dijon, France.,Laboratoire de Génétique Moléculaire, PTB, CHU Dijon, Dijon, France
| | - Marjon van Slegtenhorst
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Laurence Faivre
- Centre de Référence maladies rares « Anomalies du Développement et syndrome malformatifs » de l'Est et Centre de Génétique, Hôpital d'Enfants, CHU, Dijon, France.,FHU-TRANSLAD, Université de Bourgogne/CHU Dijon, Dijon, France.,Equipe EA4271 GAD, Université de Bourgogne, Dijon, France
| | - Amélie Piton
- Laboratoire de Génétique Moléculaire, CHRU Strasbourg, Strasbourg, France
| | - André Reis
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Thomas Arnesen
- Department of Molecular Biology, University of Bergen, Bergen, Norway.,Department of Surgery, Haukeland University Hospital, Bergen, Norway
| | - Christel Thauvin-Robinet
- Centre de Référence maladies rares « Anomalies du Développement et syndrome malformatifs » de l'Est et Centre de Génétique, Hôpital d'Enfants, CHU, Dijon, France.,FHU-TRANSLAD, Université de Bourgogne/CHU Dijon, Dijon, France.,Equipe EA4271 GAD, Université de Bourgogne, Dijon, France
| | - Christiane Zweier
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
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36
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Rathore OS, Faustino A, Prudêncio P, Van Damme P, Cox CJ, Martinho RG. Absence of N-terminal acetyltransferase diversification during evolution of eukaryotic organisms. Sci Rep 2016; 6:21304. [PMID: 26861501 PMCID: PMC4748286 DOI: 10.1038/srep21304] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 01/18/2016] [Indexed: 11/09/2022] Open
Abstract
Protein N-terminal acetylation is an ancient and ubiquitous co-translational modification catalyzed by a highly conserved family of N-terminal acetyltransferases (NATs). Prokaryotes have at least 3 NATs, whereas humans have six distinct but highly conserved NATs, suggesting an increase in regulatory complexity of this modification during eukaryotic evolution. Despite this, and against our initial expectations, we determined that NAT diversification did not occur in the eukaryotes, as all six major human NATs were most likely present in the Last Eukaryotic Common Ancestor (LECA). Furthermore, we also observed that some NATs were actually secondarily lost during evolution of major eukaryotic lineages; therefore, the increased complexity of the higher eukaryotic proteome occurred without a concomitant diversification of NAT complexes.
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Affiliation(s)
- Om Singh Rathore
- Department of Biomedical Sciences and Medicine, Faro, Portugal.,Center for Biomedical Research (CBMR), Faro, Portugal.,ProRegeM-PhD Program in Mechanisms of Disease and Regenerative Medicine, Faro, Portugal
| | - Alexandra Faustino
- Department of Biomedical Sciences and Medicine, Faro, Portugal.,Center for Biomedical Research (CBMR), Faro, Portugal
| | - Pedro Prudêncio
- Department of Biomedical Sciences and Medicine, Faro, Portugal.,Center for Biomedical Research (CBMR), Faro, Portugal.,Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, Oeiras 2781-901, Portugal
| | - Petra Van Damme
- Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium.,Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Cymon J Cox
- Center of Marine Sciences, University of Algarve, Faro, Portugal
| | - Rui Gonçalo Martinho
- Department of Biomedical Sciences and Medicine, Faro, Portugal.,Center for Biomedical Research (CBMR), Faro, Portugal.,Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, Oeiras 2781-901, Portugal
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37
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Casey JP, Støve SI, McGorrian C, Galvin J, Blenski M, Dunne A, Ennis S, Brett F, King MD, Arnesen T, Lynch SA. NAA10 mutation causing a novel intellectual disability syndrome with Long QT due to N-terminal acetyltransferase impairment. Sci Rep 2015; 5:16022. [PMID: 26522270 PMCID: PMC4629191 DOI: 10.1038/srep16022] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 10/08/2015] [Indexed: 12/03/2022] Open
Abstract
We report two brothers from a non-consanguineous Irish family presenting with a novel syndrome characterised by intellectual disability, facial dysmorphism, scoliosis and long QT. Their mother has a milder phenotype including long QT. X-linked inheritance was suspected. Whole exome sequencing identified a novel missense variant (c.128 A > C; p.Tyr43Ser) in NAA10 (X chromosome) as the cause of the family’s disorder. Sanger sequencing confirmed that the mutation arose de novo in the carrier mother. NAA10 encodes the catalytic subunit of the major human N-terminal acetylation complex NatA. In vitro assays for the p.Tyr43Ser mutant enzyme showed a significant decrease in catalytic activity and reduced stability compared to wild-type Naa10 protein. NAA10 has previously been associated with Ogden syndrome, Lenz microphthalmia syndrome and non-syndromic developmental delay. Our findings expand the clinical spectrum of NAA10 and suggest that the proposed correlation between mutant Naa10 enzyme activity and phenotype severity is more complex than anticipated; the p.Tyr43Ser mutant enzyme has less catalytic activity than the p.Ser37Pro mutant associated with lethal Ogden syndrome but results in a milder phenotype. Importantly, we highlight the need for cardiac assessment in males and females with NAA10 variants as both patients and carriers can have long QT.
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Affiliation(s)
- Jillian P Casey
- Clinical Genetics, Temple Street Children's University Hospital, Temple Street, Dublin 1, Ireland.,UCD Academic Centre on Rare Diseases, School of Medicine and Medical Sciences, University College Dublin, Dublin 4, Ireland
| | - Svein I Støve
- Department of Molecular Biology, University of Bergen, Norway
| | - Catherine McGorrian
- Department of Cardiology, Mater Misericordiae University Hospital, Eccles Street, Dublin 7, Ireland.,School of Medicine and Medical Sciences, University College Dublin, Dublin 4, Ireland
| | - Joseph Galvin
- Department of Cardiology, Mater Misericordiae University Hospital, Eccles Street, Dublin 7, Ireland
| | - Marina Blenski
- Department of Molecular Biology, University of Bergen, Norway
| | - Aimee Dunne
- UCD Academic Centre on Rare Diseases, School of Medicine and Medical Sciences, University College Dublin, Dublin 4, Ireland
| | - Sean Ennis
- UCD Academic Centre on Rare Diseases, School of Medicine and Medical Sciences, University College Dublin, Dublin 4, Ireland
| | - Francesca Brett
- Department of Neuropathology, Beaumont Hospital, Dublin 9, Ireland
| | - Mary D King
- Department of Paediatric Neurology &Clinical Neurophysiology, Temple Street Children's University Hospital, Dublin 1, Ireland.,UCD Academic Centre on Rare Diseases, School of Medicine and Medical Sciences, University College Dublin, Dublin 4, Ireland
| | - Thomas Arnesen
- Department of Molecular Biology, University of Bergen, Norway.,Department of Surgery, Haukeland University Hospital, Norway
| | - Sally Ann Lynch
- Clinical Genetics, Temple Street Children's University Hospital, Temple Street, Dublin 1, Ireland.,UCD Academic Centre on Rare Diseases, School of Medicine and Medical Sciences, University College Dublin, Dublin 4, Ireland.,Our Lady's Children's Hospital, Crumlin, Dublin 12, Ireland
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38
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Varland S, Osberg C, Arnesen T. N-terminal modifications of cellular proteins: The enzymes involved, their substrate specificities and biological effects. Proteomics 2015; 15:2385-401. [PMID: 25914051 PMCID: PMC4692089 DOI: 10.1002/pmic.201400619] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 03/04/2015] [Accepted: 04/21/2015] [Indexed: 01/18/2023]
Abstract
The vast majority of eukaryotic proteins are N-terminally modified by one or more processing enzymes. Enzymes acting on the very first amino acid of a polypeptide include different peptidases, transferases, and ligases. Methionine aminopeptidases excise the initiator methionine leaving the nascent polypeptide with a newly exposed amino acid that may be further modified. N-terminal acetyl-, methyl-, myristoyl-, and palmitoyltransferases may attach an acetyl, methyl, myristoyl, or palmitoyl group, respectively, to the α-amino group of the target protein N-terminus. With the action of ubiquitin ligases, one or several ubiquitin molecules are transferred, and hence, constitute the N-terminal modification. Modifications at protein N-termini represent an important contribution to proteomic diversity and complexity, and are essential for protein regulation and cellular signaling. Consequently, dysregulation of the N-terminal modifying enzymes is implicated in human diseases. We here review the different protein N-terminal modifications occurring co- or post-translationally with emphasis on the responsible enzymes and their substrate specificities.
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Affiliation(s)
- Sylvia Varland
- Department of Molecular Biology, University of Bergen, Bergen, Norway
| | - Camilla Osberg
- Department of Molecular Biology, University of Bergen, Bergen, Norway.,Department of Surgery, Haukeland University Hospital, Bergen, Norway
| | - Thomas Arnesen
- Department of Molecular Biology, University of Bergen, Bergen, Norway.,Department of Surgery, Haukeland University Hospital, Bergen, Norway
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39
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Van Damme P, Hole K, Gevaert K, Arnesen T. N-terminal acetylome analysis reveals the specificity of Naa50 (Nat5) and suggests a kinetic competition between N-terminal acetyltransferases and methionine aminopeptidases. Proteomics 2015; 15:2436-46. [PMID: 25886145 DOI: 10.1002/pmic.201400575] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 03/04/2015] [Accepted: 04/14/2015] [Indexed: 11/08/2022]
Abstract
Cotranslational N-terminal (Nt-) acetylation of nascent polypeptides is mediated by N-terminal acetyltransferases (NATs). The very N-terminal amino acid sequence largely determines whether or not a given protein is Nt-acetylated. Currently, there are six distinct NATs characterized, NatA-NatF, in humans of which the in vivo substrate specificity of Naa50 (Nat5)/NatE, an alternative catalytic subunit of the human NatA, so far remained elusive. In this study, we quantitatively compared the Nt-acetylomes of wild-type yeast S. cerevisiae expressing the endogenous yeast Naa50 (yNaa50), the congenic strain lacking yNaa50, and an otherwise identical strain expressing human Naa50 (hNaa50). Six canonical yeast NatA substrates were Nt-acetylated less in yeast lacking yNaa50 than in wild-type yeast. In contrast, the ectopically expressed hNaa50 resulted, predominantly, in the Nt-acetylation of N-terminal Met (iMet) starting N-termini, including iMet-Lys, iMet-Val, iMet-Ala, iMet-Tyr, iMet-Phe, iMet-Leu, iMet-Ser, and iMet-Thr N-termini. This identified hNaa50 as being similar, in its substrate specificity, to the previously characterized hNaa60/NatF. In addition, the identification, in yNaa50-lacking yeast expressing hNaa50, of Nt-acetylated iMet followed by a small residue such as Ser, Thr, Ala, or Val, revealed a kinetic competition between Naa50 and Met-aminopeptidases (MetAPs), and implied that Nt-acetylated iMet followed by a small residue cannot be removed by MetAPs, a deduction supported by our in vitro data. As such, Naa50-mediated Nt-acetylation may act to retain the iMet of proteins of otherwise MetAP susceptible N-termini and the fraction of retained and Nt-acetylated iMet (followed by a small residue) in such a setting would be expected to depend on the relative levels of ribosome-associated Naa50/NatA and MetAPs.
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Affiliation(s)
- Petra Van Damme
- Department of Medical Protein Research, VIB, Ghent, Belgium.,Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Kristine Hole
- Department of Molecular Biology, University of Bergen, Bergen, Norway.,Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Kris Gevaert
- Department of Medical Protein Research, VIB, Ghent, Belgium.,Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Thomas Arnesen
- Department of Molecular Biology, University of Bergen, Bergen, Norway.,Department of Surgery, Haukeland University Hospital, Bergen, Norway
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40
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The biological functions of Naa10 - From amino-terminal acetylation to human disease. Gene 2015; 567:103-31. [PMID: 25987439 DOI: 10.1016/j.gene.2015.04.085] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 04/20/2015] [Accepted: 04/27/2015] [Indexed: 01/07/2023]
Abstract
N-terminal acetylation (NTA) is one of the most abundant protein modifications known, and the N-terminal acetyltransferase (NAT) machinery is conserved throughout all Eukarya. Over the past 50 years, the function of NTA has begun to be slowly elucidated, and this includes the modulation of protein-protein interaction, protein-stability, protein function, and protein targeting to specific cellular compartments. Many of these functions have been studied in the context of Naa10/NatA; however, we are only starting to really understand the full complexity of this picture. Roughly, about 40% of all human proteins are substrates of Naa10 and the impact of this modification has only been studied for a few of them. Besides acting as a NAT in the NatA complex, recently other functions have been linked to Naa10, including post-translational NTA, lysine acetylation, and NAT/KAT-independent functions. Also, recent publications have linked mutations in Naa10 to various diseases, emphasizing the importance of Naa10 research in humans. The recent design and synthesis of the first bisubstrate inhibitors that potently and selectively inhibit the NatA/Naa10 complex, monomeric Naa10, and hNaa50 further increases the toolset to analyze Naa10 function.
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41
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Protein amino-terminal modifications and proteomic approaches for N-terminal profiling. Curr Opin Chem Biol 2015; 24:71-9. [DOI: 10.1016/j.cbpa.2014.10.026] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 10/27/2014] [Accepted: 10/28/2014] [Indexed: 01/24/2023]
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42
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Molecular, Cellular, and Physiological Significance of N-Terminal Acetylation. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2015; 316:267-305. [DOI: 10.1016/bs.ircmb.2015.01.001] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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43
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Myklebust LM, Van Damme P, Støve SI, Dörfel MJ, Abboud A, Kalvik TV, Grauffel C, Jonckheere V, Wu Y, Swensen J, Kaasa H, Liszczak G, Marmorstein R, Reuter N, Lyon GJ, Gevaert K, Arnesen T. Biochemical and cellular analysis of Ogden syndrome reveals downstream Nt-acetylation defects. Hum Mol Genet 2014; 24:1956-76. [PMID: 25489052 PMCID: PMC4355026 DOI: 10.1093/hmg/ddu611] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The X-linked lethal Ogden syndrome was the first reported human genetic disorder associated with a mutation in an N-terminal acetyltransferase (NAT) gene. The affected males harbor an Ser37Pro (S37P) mutation in the gene encoding Naa10, the catalytic subunit of NatA, the major human NAT involved in the co-translational acetylation of proteins. Structural models and molecular dynamics simulations of the human NatA and its S37P mutant highlight differences in regions involved in catalysis and at the interface between Naa10 and the auxiliary subunit hNaa15. Biochemical data further demonstrate a reduced catalytic capacity and an impaired interaction between hNaa10 S37P and Naa15 as well as Naa50 (NatE), another interactor of the NatA complex. N-Terminal acetylome analyses revealed a decreased acetylation of a subset of NatA and NatE substrates in Ogden syndrome cells, supporting the genetic findings and our hypothesis regarding reduced Nt-acetylation of a subset of NatA/NatE-type substrates as one etiology for Ogden syndrome. Furthermore, Ogden syndrome fibroblasts display abnormal cell migration and proliferation capacity, possibly linked to a perturbed retinoblastoma pathway. N-Terminal acetylation clearly plays a role in Ogden syndrome, thus revealing the in vivo importance of N-terminal acetylation in human physiology and disease.
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Affiliation(s)
- Line M Myklebust
- Department of Molecular Biology, University of Bergen, Bergen N-5020, Norway
| | - Petra Van Damme
- Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium, Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium,
| | - Svein I Støve
- Department of Molecular Biology, University of Bergen, Bergen N-5020, Norway, Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway
| | - Max J Dörfel
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Woodbury, NY 11797, USA
| | - Angèle Abboud
- Department of Molecular Biology, University of Bergen, Bergen N-5020, Norway, Computational Biology Unit, Uni Computing, Uni Research AS, Bergen, Norway
| | - Thomas V Kalvik
- Department of Molecular Biology, University of Bergen, Bergen N-5020, Norway
| | - Cedric Grauffel
- Department of Molecular Biology, University of Bergen, Bergen N-5020, Norway, Computational Biology Unit, Uni Computing, Uni Research AS, Bergen, Norway
| | - Veronique Jonckheere
- Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium, Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Yiyang Wu
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Woodbury, NY 11797, USA, Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY 11794, USA
| | | | - Hanna Kaasa
- Department of Molecular Biology, University of Bergen, Bergen N-5020, Norway
| | - Glen Liszczak
- Program in Gene Expression and Regulation, Wistar Institute, PA 19104, USA, Department of Chemistry, and Department of Biochemistry and Biophysics and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ronen Marmorstein
- Program in Gene Expression and Regulation, Wistar Institute, PA 19104, USA, Department of Chemistry, and Department of Biochemistry and Biophysics and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nathalie Reuter
- Department of Molecular Biology, University of Bergen, Bergen N-5020, Norway, Computational Biology Unit, Uni Computing, Uni Research AS, Bergen, Norway
| | - Gholson J Lyon
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Woodbury, NY 11797, USA, Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY 11794, USA,
| | - Kris Gevaert
- Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium, Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Thomas Arnesen
- Department of Molecular Biology, University of Bergen, Bergen N-5020, Norway, Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway,
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44
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Gawron D, Gevaert K, Van Damme P. The proteome under translational control. Proteomics 2014; 14:2647-62. [PMID: 25263132 DOI: 10.1002/pmic.201400165] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 08/21/2014] [Accepted: 09/23/2014] [Indexed: 02/02/2023]
Abstract
A single eukaryotic gene can give rise to a variety of protein forms (proteoforms) as a result of genetic variation and multilevel regulation of gene expression. In addition to alternative splicing, an increasing line of evidence shows that alternative translation contributes to the overall complexity of proteomes. Identifying the repertoire of proteins and micropeptides expressed by alternative selection of (near-)cognate translation initiation sites and different reading frames however remains challenging with contemporary proteomics. MS-enabled identification of proteoforms is expected to benefit from transcriptome and translatome data by the creation of customized and sample-specific protein sequence databases. Here, we focus on contemporary integrative omics approaches that complement proteomics with DNA- and/or RNA-oriented technologies to elucidate the mechanisms of translational control. Together, these technologies enable to map the translation (initiation) landscape and more comprehensively define the inventory of proteoforms raised upon alternative translation, thus assisting in the (re-)annotation of genomes.
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Affiliation(s)
- Daria Gawron
- Department of Medical Protein Research, VIB, Ghent, Belgium; Department of Biochemistry, Ghent University, Ghent, Belgium
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45
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De novo missense mutations in the NAA10 gene cause severe non-syndromic developmental delay in males and females. Eur J Hum Genet 2014; 23:602-9. [PMID: 25099252 PMCID: PMC4402627 DOI: 10.1038/ejhg.2014.150] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 06/13/2014] [Accepted: 06/20/2014] [Indexed: 12/30/2022] Open
Abstract
Recent studies revealed the power of whole-exome sequencing to identify mutations in sporadic cases with non-syndromic intellectual disability. We now identified de novo missense variants in NAA10 in two unrelated individuals, a boy and a girl, with severe global developmental delay but without any major dysmorphism by trio whole-exome sequencing. Both de novo variants were predicted to be deleterious, and we excluded other variants in this gene. This X-linked gene encodes N-alpha-acetyltransferase 10, the catalytic subunit of the NatA complex involved in multiple cellular processes. A single hypomorphic missense variant p.(Ser37Pro) was previously associated with Ogden syndrome in eight affected males from two different families. This rare disorder is characterized by a highly recognizable phenotype, global developmental delay and results in death during infancy. In an attempt to explain the discrepant phenotype, we used in vitro N-terminal acetylation assays which suggested that the severity of the phenotype correlates with the remaining catalytic activity. The variant in the Ogden syndrome patients exhibited a lower activity than the one seen in the boy with intellectual disability, while the variant in the girl was the most severe exhibiting only residual activity in the acetylation assays used. We propose that N-terminal acetyltransferase deficiency is clinically heterogeneous with the overall catalytic activity determining the phenotypic severity.
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Holmes WM, Mannakee BK, Gutenkunst RN, Serio TR. Loss of amino-terminal acetylation suppresses a prion phenotype by modulating global protein folding. Nat Commun 2014; 5:4383. [PMID: 25023910 PMCID: PMC4140192 DOI: 10.1038/ncomms5383] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 06/13/2014] [Indexed: 01/08/2023] Open
Abstract
N-terminal acetylation is among the most ubiquitous of protein modifications in eukaryotes. While loss of N-terminal acetylation is associated with many abnormalities, the molecular basis of these effects is known for only a few cases, where acetylation of single factors has been linked to binding avidity or metabolic stability. In contrast, the impact of N-terminal acetylation for the majority of the proteome, and its combinatorial contributions to phenotypes, are unknown. Here, by studying the yeast prion [PSI+], an amyloid of the Sup35 protein, we show that loss of N-terminal acetylation promotes general protein misfolding, a redeployment of chaperones to these substrates, and a corresponding stress response. These proteostasis changes, combined with the decreased stability of unacetylated Sup35 amyloid, reduce the size of prion aggregates and reverse their phenotypic consequences. Thus, loss of N-terminal acetylation, and its previously unanticipated role in protein biogenesis, globally resculpts the proteome to create a unique phenotype.
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Affiliation(s)
- William M Holmes
- 1] Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, 185 Meeting Street, Providence, Rhode Island 02912, USA [2]
| | - Brian K Mannakee
- Graduate Interdisciplinary Program in Statistics, University of Arizona, 1548 East Drachman Street, Tucson, Arizona 85721, USA
| | - Ryan N Gutenkunst
- Department of Molecular and Cellular Biology, University of Arizona, 1007 East Lowell Street, Tucson, Arizona 85721, USA
| | - Tricia R Serio
- 1] Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, 185 Meeting Street, Providence, Rhode Island 02912, USA [2]
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